COLLECTIVE VARIABLES MODULE

Reference manual for VMD

Code version: 2018-06-06

Alejandro Bernardin, Jeﬀrey R. Comer, Giacomo Fiorin, Haohao Fu, Jérôme Hénin, Axel Kohlmeyer, Fabrizio Marinelli, Joshua V. Vermaas, Andrew D. White

1 Introduction

2 A crash course

3 General parameters and input/output ﬁles

3.1 Using the cv command

3.1.1 Example use of the cv command: analyze a trajectory

3.1.2 Managing the Colvars module

3.1.3 Input and output

3.1.4 Accessing collective variables

3.1.5 Accessing biases

3.2 Conﬁguration syntax for the Colvars module

3.3 Input state ﬁle (optional)

3.4 Output ﬁles

4 Deﬁning and setting up collective variables

4.1 General options for a collective variable

4.2 Trajectory output

4.3 Extended Lagrangian.

4.4 Statistical analysis of collective variables

5 Selecting atoms

5.1 Atom selection keywords

5.2 Moving frame of reference.

5.3 Treatment of periodic boundary conditions.

5.4 Performance of a Colvars calculation based on group size.

6 Collective variable types (available functions)

6.1 List of available colvar components

6.1.1 distance: center-of-mass distance between two groups.

6.1.2 distanceZ: projection of a distance vector on an axis.

6.1.3 distanceXY: modulus of the projection of a distance vector on a plane.

6.1.4 distanceVec: distance vector between two groups.

6.1.5 distanceDir: distance unit vector between two groups.

6.1.6 distanceInv: mean distance between two groups of atoms.

6.1.7 distancePairs: set of pairwise distances between two groups.

6.1.8 cartesian: vector of atomic Cartesian coordinates.

6.1.9 angle: angle between three groups.

6.1.10 dipoleAngle: angle between two groups and dipole of a third group.

6.1.11 dihedral: torsional angle between four groups.

6.1.12 polarTheta: polar angle in spherical coordinates.

6.1.13 polarPhi: azimuthal angle in spherical coordinates.

6.1.14 coordNum: coordination number between two groups.

6.1.15 selfCoordNum: coordination number between atoms within a group.

6.1.16 hBond: hydrogen bond between two atoms.

6.1.17 rmsd: root mean square displacement (RMSD) from reference positions.

6.1.18 Advanced usage of the rmsd component.

6.1.19 eigenvector: projection of the atomic coordinates on a vector.

6.1.20 gyration: radius of gyration of a group of atoms.

6.1.21 inertia: total moment of inertia of a group of atoms.

6.1.22 inertiaZ: total moment of inertia of a group of atoms around a chosen axis.

6.1.23 orientation: orientation from reference coordinates.

6.1.24 orientationAngle: angle of rotation from reference coordinates.

6.1.25 orientationProj: cosine of the angle of rotation from reference coordinates.

6.1.26 spinAngle: angle of rotation around a given axis.

6.1.27 tilt: cosine of the rotation orthogonal to a given axis.

6.1.28 alpha: α-helix content of a protein segment.

6.1.29 dihedralPC: protein dihedral pricipal component

6.2 Conﬁguration keywords shared by all components

6.3 Advanced usage and special considerations

6.3.1 Periodic components.

6.3.2 Non-scalar components.

6.3.3 Calculating total forces.

6.4 Linear and polynomial combinations of components

6.5 Colvars as scripted functions of components

7 Biasing and analysis methods

7.1 Adaptive Biasing Force

7.1.1 ABF requirements on collective variables

7.1.2 Parameters for ABF

7.1.3 Output ﬁles

7.1.4 Post-processing: reconstructing a multidimensional free energy surface

7.2 Extended-system Adaptive Biasing Force (eABF)

7.2.1 CZAR estimator of the free energy

7.3 Metadynamics

7.3.1 Output ﬁles

7.3.2 Performance tuning

7.3.3 Well-tempered metadynamics

7.3.4 Multiple-replicas metadynamics

7.3.5 Compatibility and post-processing

7.4 Harmonic restraints

7.4.1 Moving restraints: steered molecular dynamics

7.4.2 Moving restraints: umbrella sampling

7.4.3 Changing force constant

7.5 Computing the work of a changing restraint

7.6 Harmonic wall restraints

7.7 Linear restraints

7.8 Adaptive Linear Bias/Experiment Directed Simulation

7.9 Multidimensional histograms

7.9.1 Grid deﬁnition for multidimensional histograms

7.10 Probability distribution-restraints

7.11 Scripted biases

2 A crash course

3 General parameters and input/output ﬁles

3.1 Using the cv command

3.1.1 Example use of the cv command: analyze a trajectory

3.1.2 Managing the Colvars module

3.1.3 Input and output

3.1.4 Accessing collective variables

3.1.5 Accessing biases

3.2 Conﬁguration syntax for the Colvars module

3.3 Input state ﬁle (optional)

3.4 Output ﬁles

4 Deﬁning and setting up collective variables

4.1 General options for a collective variable

4.2 Trajectory output

4.3 Extended Lagrangian.

4.4 Statistical analysis of collective variables

5 Selecting atoms

5.1 Atom selection keywords

5.2 Moving frame of reference.

5.3 Treatment of periodic boundary conditions.

5.4 Performance of a Colvars calculation based on group size.

6 Collective variable types (available functions)

6.1 List of available colvar components

6.1.1 distance: center-of-mass distance between two groups.

6.1.2 distanceZ: projection of a distance vector on an axis.

6.1.3 distanceXY: modulus of the projection of a distance vector on a plane.

6.1.4 distanceVec: distance vector between two groups.

6.1.5 distanceDir: distance unit vector between two groups.

6.1.6 distanceInv: mean distance between two groups of atoms.

6.1.7 distancePairs: set of pairwise distances between two groups.

6.1.8 cartesian: vector of atomic Cartesian coordinates.

6.1.9 angle: angle between three groups.

6.1.10 dipoleAngle: angle between two groups and dipole of a third group.

6.1.11 dihedral: torsional angle between four groups.

6.1.12 polarTheta: polar angle in spherical coordinates.

6.1.13 polarPhi: azimuthal angle in spherical coordinates.

6.1.14 coordNum: coordination number between two groups.

6.1.15 selfCoordNum: coordination number between atoms within a group.

6.1.16 hBond: hydrogen bond between two atoms.

6.1.17 rmsd: root mean square displacement (RMSD) from reference positions.

6.1.18 Advanced usage of the rmsd component.

6.1.19 eigenvector: projection of the atomic coordinates on a vector.

6.1.20 gyration: radius of gyration of a group of atoms.

6.1.21 inertia: total moment of inertia of a group of atoms.

6.1.22 inertiaZ: total moment of inertia of a group of atoms around a chosen axis.

6.1.23 orientation: orientation from reference coordinates.

6.1.24 orientationAngle: angle of rotation from reference coordinates.

6.1.25 orientationProj: cosine of the angle of rotation from reference coordinates.

6.1.26 spinAngle: angle of rotation around a given axis.

6.1.27 tilt: cosine of the rotation orthogonal to a given axis.

6.1.28 alpha: α-helix content of a protein segment.

6.1.29 dihedralPC: protein dihedral pricipal component

6.2 Conﬁguration keywords shared by all components

6.3 Advanced usage and special considerations

6.3.1 Periodic components.

6.3.2 Non-scalar components.

6.3.3 Calculating total forces.

6.4 Linear and polynomial combinations of components

6.5 Colvars as scripted functions of components

7 Biasing and analysis methods

7.1 Adaptive Biasing Force

7.1.1 ABF requirements on collective variables

7.1.2 Parameters for ABF

7.1.3 Output ﬁles

7.1.4 Post-processing: reconstructing a multidimensional free energy surface

7.2 Extended-system Adaptive Biasing Force (eABF)

7.2.1 CZAR estimator of the free energy

7.3 Metadynamics

7.3.1 Output ﬁles

7.3.2 Performance tuning

7.3.3 Well-tempered metadynamics

7.3.4 Multiple-replicas metadynamics

7.3.5 Compatibility and post-processing

7.4 Harmonic restraints

7.4.1 Moving restraints: steered molecular dynamics

7.4.2 Moving restraints: umbrella sampling

7.4.3 Changing force constant

7.5 Computing the work of a changing restraint

7.6 Harmonic wall restraints

7.7 Linear restraints

7.8 Adaptive Linear Bias/Experiment Directed Simulation

7.9 Multidimensional histograms

7.9.1 Grid deﬁnition for multidimensional histograms

7.10 Probability distribution-restraints

7.11 Scripted biases

In molecular dynamics simulations, it is often useful to reduce the large number of degrees of freedom of a physical system into few parameters whose statistical distributions can be analyzed individually, or used to deﬁne biasing potentials to alter the dynamics of the system in a controlled manner. These have been called ‘order parameters’, ‘collective variables’, ‘(surrogate) reaction coordinates’, and many other terms.

Here we use primarily the term ‘collective variable’ (shortened to colvar), which indicates any
diﬀerentiable function of atomic Cartesian coordinates, x_{i}, with i between 1 and N, the total number of
atoms:

| (1) |

This manual documents the collective variables module (Colvars), a portable software that interfaces multiple MD simulation programs, with a focus on ﬂexibility, robustness and high performance. The module is designed to perform multiple tasks concurrently during or after a simulation, the most common of which are:

- apply restraints or biasing potentials to multiple colvars, tailored on the system by choosing from a wide set of basis functions, without limitations on their number or on the number of atoms involved;
- calculate potentials of mean force (PMFs) along any set of colvars, using diﬀerent enhanced sampling methods, such as Adaptive Biasing Force (ABF), metadynamics, steered MD and umbrella sampling; variants of these methods that make use of an ensemble of replicas are supported as well;
- calculate statistical properties of the colvars, such as running averages and standard deviations, correlation functions of pairs of colvars, and multidimensional histograms: this can be done either at run-time without the need to save very large trajectory ﬁles, or after a simulation has been completed using VMD and the cv command.

Note: although restraints and PMF algorithms are primarily used during simulations, they are also available in VMD to test a new input for a simulation, or to evaluate the relative free energy of a new structure based on data from a previous calculation. Options that only have an eﬀect during a simulation are also included for compatibility purposes.

Detailed explanations of the design of the Colvars module are provided in reference [1]. Please cite this reference whenever publishing work that makes use of this module.

Suppose that we want to run a steered MD experiment where a small molecule is pulled away from a binding site. In Colvars terms, this is done by applying a moving restraint to the distance between the two objects. The conﬁguration will contain two blocks, one deﬁning the distance variable (see sections 4 and 6), and the other the moving harmonic restraint (7.4).

colvar {

name dist

distance {

group1 { atomNumbersRange 42-55 }

group2 {

psfSegID PR

atomNameResidueRange CA 15-30 }

}

}

}

harmonic {

colvars dist

forceConstant 20.0

centers 4. # initial distance

targetCenters 15. # final distance

targetNumSteps 500000

}

Reading this input in plain English: the variable here named dist consists in a distance function between the centers of two groups: the ligand (atoms 42 to 55) and the alpha carbon atoms (CA) of residues 15 to 30 in the protein (segment name PR). The atom selection syntax is detailed in section 5.

To the “dist” variable, we apply a harmonic potential of force constant 20 kcal/mol/Å^{2}, initially centered
around a value of 4 Å, which will increase to 15 Å over 500,000 simulation steps.

Here, we document the syntax of the commands and parameters used to set up and use the Colvars module in VMD. One of these parameters is the conﬁguration ﬁle or the conﬁguration text for the module itself, whose syntax is described in 3.2 and in the following sections.

The Colvars module is accessed in VMD through the command cv. The command must be used the ﬁrst time as cv molid <molid> to set up the Colvars module for a given molecule. In all following uses, the cv command will continue operating on the same molecule, regardless of its “top” status. To use the cv command on a diﬀerent molecule, use cv delete ﬁrst and then cv molid <molid>. Invoking the cv command with no arguments prints a help screen.

Collective variables and biases can be added, queried and deleted through the scripting command cv, with the following syntax: cv <subcommand> [args...]. For example, to query the value of a collective variable named myVar, use the following syntax: set value [cv colvar myVar value]. All subcommands of cv are documented below.

By far the most typical use of Colvars in VMD is computing the values of one or more variables along an
existing trajectory:

# Activate the module on the current VMD molecule

cv molid top

# Load a Colvars config file

cv configfile test.in

set out [open "test.colvars.traj" "w"]

# Write the labels to the file

puts -nonewline ${out} [cv printframelabels]

for { set fr 0 } { ${fr} } { incr fr } {

# Point Colvars to this trajectory frame

cv frame ${fr}

# Recompute variables and biases

cv update

# Print variables and biases to the file

puts -nonewline ${out} [cv printframe]

}

close ${out}

The following sections explain the syntax of the various sub-commands of cv.

- molid <molid>: setup the Colvars module for the given molecule; <molid> is the identiﬁer of a valid VMD molecule, either an integer or top for the top molecule;
- delete: delete the Colvars module; after this, the module can be setup again using cv molid;
- configfile <ﬁle name>: read conﬁguration from a ﬁle;
- config <string>: read conﬁguration from the given string; both config and configfile subcommands may be invoked multiple times; see 3.2 for the conﬁguration syntax;
- reset: delete all internal conﬁguration of the Colvars module;
- version: return the version of the colvars code.

- list: return a list of all currently deﬁned variables; See 4, 6 and 5 for how to conﬁgure a collective variable;
- list biases: return a list of all currently deﬁned biases (i.e. sampling and analysis algorithms);
- load <ﬁle name>: load a collective variables state ﬁle, typically produced during a previous simulation; this parameter requires that the corresponding conﬁguration has already been loaded by configfile or config; see 3.4 for a brief description of this ﬁle; the contents of this ﬁle are not required for as long as the VMD molecule has valid coordinates and cv update is used;
- load <preﬁx>: same as above, but without the .colvars.state suﬃx;
- save <preﬁx>: save the current state in a ﬁle whose name begins with the given argument; if any of the biases have additional output ﬁles deﬁned, those are saved as well using the same preﬁx;
- update: recalculate all colvars and biases based on the current atomic coordinates;
- addenergy<E>: add value E to the total bias energy; this must be used within calc_colvar_forces;
- printframe: return a summary of the current frame, in a format equivalent to a line of the collective variables trajectory ﬁle;
- printframelabels: return text labels for the columns of printframe’s output;
- frame: return the current frame number, from which colvar values are calculated;
- frame <new frame>: set the frame number; returns 0 if successful, nonzero if the requested frame does not exist.

- colvar <name> value: return the current value of colvar <name>;
- colvar <name> update: recalculate colvar <name>;
- colvar <name> type: return the type of colvar <name>;
- colvar <name> delete: delete colvar <name>;
- colvar <name> getconfig: return conﬁg string of colvar <name>.
- colvar <name> cvcflags <ﬂags>: for a colvar with several CVCs (numbered according to their name string order), set which CVCs are enabled or disabled in subsequent evaluations according to a list of 0/1 ﬂags (one per CVC).
- colvar <name> modifycvcs <strings>: for a colvar with one or more CVCs (numbered according to their name string order), pass a list of new conﬁguration strings to modify each CVC without needing to delete the colvar. This option is currently limited to changing the values of componentCoeff and componentExp (e.g. to update the polynomial superposition parameters on the ﬂy), of period and wrapAround (e.g. to update the period of variables such as distanceZ), and of the forceNoPBC option for those CVCs that support it. Changes in conﬁguration done by this command are not saved to state ﬁles, and are lost when restarting a simulation, deleting the parent colvar, or resetting the module with cv delete or cv reset.

- bias <name> energy: return the current energy of the bias <name>;
- bias <name> update: recalculate the bias <name>;
- bias <name> delete: delete the bias <name>;
- bias <name> getconfig: return conﬁg string of bias <name>.

The Colvars conﬁguration is usually read using the commands cv configfile or cv config. The syntax of the Colvars conﬁguration is “keyword value”, where the keyword and its value are separated by any white space. The following rules apply:

- keywords are case-insensitive (upperBoundary is the same as upperboundary and UPPERBOUNDARY): their string values are however case-sensitive (e.g. ﬁle names);
- a long value or a list of multiple values can be distributed across multiple lines by using curly braces, “{” and “}”: the opening brace “{” must occur on the same line as the keyword, following a space character or other white space; the closing brace “}” can be at any position after that;
- many keywords are nested, and are only meaningful within a speciﬁc context: for every keyword documented in the following, the “parent” keyword that deﬁnes such context is also indicated;
- Tcl syntax is generally not available, but it is possible to use Tcl variables or bracket expansion of commands within a conﬁguration string, when this is passed via the command cv config …: for example, it is possible to convert the atom selection $sel into an atom group (see 5.1) using cv config "atomNumbers { [$sel get serial] }";
- if a keyword requiring a boolean value (yes|on|true or no|off|false) is provided without an explicit value, it defaults to ‘yes|on|true’; for example, ‘outputAppliedForce’ may be used as shorthand for ‘outputAppliedForce on’;
- the hash character # indicates a comment: all text in the same line following this character will be ignored.

The following keywords are available in the global context of the Colvars conﬁguration, i.e. they are not nested inside other keywords:

- colvarsTrajFrequency ⟨Colvar value trajectory frequency⟩

Context: global

Acceptable values: positive integer

Default value: 100

Description: The values of each colvar (and of other related quantities, if requested) are written to the ﬁle outputName.colvars.traj every these many steps throughout the simulation. If the value is 0, such trajectory ﬁle is not written. For optimization the output is buﬀered, and synchronized with the disk only when the restart ﬁle is being written. - colvarsRestartFrequency ⟨Colvar module restart frequency⟩

Context: global

Acceptable values: positive integer

Default value: restartFreq

Description: Allows to choose a diﬀerent restart frequency for the Colvars module. Redeﬁning it may be useful to trace the time evolution of those few properties which are not written to the trajectory ﬁle for reasons of disk space. - indexFile ⟨Index ﬁle for atom selection (GROMACS “ndx” format)⟩

Context: global

Acceptable values: UNIX ﬁlename

Description: This option reads an index ﬁle (usually with a .ndx extension) as produced by the make_ndx tool of GROMACS. This keyword may be repeated to load multiple index ﬁles: the same group name cannot appear in multiple index ﬁles. The names of index groups contained in this ﬁle can then be used to deﬁne atom groups with the indexGroup keyword. Other supported methods to select atoms are described in 5. - smp ⟨Whether SMP parallelism should be used⟩

Context: global

Acceptable values: boolean

Default value: on

Description: If this ﬂag is enabled (default), SMP parallelism over threads will be used to compute variables and biases, provided that this is supported by the VMD build in use. - analysis ⟨Turn on run-time statistical analysis⟩

Context: global

Acceptable values: boolean

Default value: off

Description: If this ﬂag is enabled, each colvar is instructed to perform whatever run-time statistical analysis it is conﬁgured to, such as correlation functions, or running averages and standard deviations. See section 4.4 for details.

To illustrate the ﬂexibility of the Colvars module, a non-trivial setup is represented in Figure 1. The
corresponding conﬁguration is given below. The options within the colvar blocks are described in 4 and 6, those
within the harmonic and histogram blocks in 7. Note: except colvar, none of the keywords shown is
mandatory.

colvar {

# difference of two distances

name d

width 0.2 # 0.2 Å of estimated fluctuation width

distance {

componentCoeff 1.0

group1 { atomNumbers 1 2 }

group2 { atomNumbers 3 4 5 }

}

distance {

componentCoeff -1.0

group1 { atomNumbers 7 }

group2 { atomNumbers 8 9 10 }

}

}

colvar {

name c

coordNum {

cutoff 6.0

group1 { atomNumbersRange 1-10 }

group2 { atomNumbersRange 11-20 }

}

}

colvar {

name alpha

alpha {

psfSegID PROT

residueRange 1-10

}

}

harmonic {

colvars d c

centers 3.0 4.0

forceConstant 5.0

}

histogram {

colvars c alpha

}

Section 4 explains how to deﬁne a colvar and its behavior, regardless of its speciﬁc functional form. To deﬁne colvars that are appropriate to a speciﬁc physical system, Section 5 documents how to select atoms, and section 6 lists all of the available functional forms, which we call “colvar components”. Finally, section 7 lists the available methods and algorithms to perform biased simulations and multidimensional analysis of colvars.

Aside from the Colvars conﬁguration, an optional input state ﬁle may be provided to load the relevant data from a previous simulation. The name of this ﬁle is provided through cv load <ﬁle name >. This ﬁle contains information about the current run, including the number of the last computed step. .

During a simulation with collective variables deﬁned, the following three output ﬁles are written:

- a state ﬁle, named outputName.colvars.state; this ﬁle is in ASCII (plain text) format, and is meant to be used as input when continuing a simulation (see 3.3).
- if the parameter colvarsRestartFrequency is larger than zero, a restart ﬁle named restartName.colvars.state is written every that many steps: this ﬁle is equivalent to the ﬁnal state ﬁle;
- if the parameter colvarsTrajFrequency is greater than 0 (default: 100), a trajectory ﬁle is written during the simulation: its name is outputName.colvars.traj; unlike the state ﬁle, it is not needed to restart a simulation, but can be used later for post-processing and analysis.

Other output ﬁles may be written by speciﬁc methods applied to the colvars (e.g. by the ABF method, see 7.1, or the metadynamics method, see 7.3). Like the colvar trajectory ﬁle, they are needed only for analyzing, not continuing a simulation. All such ﬁles’ names also begin with the preﬁx outputName.

A collective variable is deﬁned by the keyword colvar followed by its conﬁguration options contained within curly braces:

colvar {

name xi

…

}

There are multiple ways of deﬁning a variable:

- The simplest and most common way way is using one of the precompiled functions (here called “components”), which are listed in section 6. For example, using the keyword rmsd (section 6.1.17) deﬁnes the variable as the root mean squared deviation (RMSD) of the selected atoms.
- A new variable may also be constructed as a linear or polynomial combination of the components listed in section 6 (see 6.4 for details).
- A user-deﬁned Tcl function of the existing components (see list in section 6), or of the atomic coordinates directly (see the cartesian keyword in 6.1.8). The function is provided by a separate Tcl script, and referenced through the keyword scriptedFunction (see 6.5 for details).

All components listed in section 6, including the cartesian component make use of atom selection keyword described in section 5.

The remainder of this section lists options to control the behavior of a variable, regardless of how it was deﬁned. Only the options name, width, lowerBoundary and upperBoundary are the most commonly used (4.1).

- name ⟨Name of this colvar⟩

Context: colvar

Acceptable values: string

Default value: “colvar” + numeric id

Description: The name is an unique case-sensitive string which allows the Colvars module to identify this colvar unambiguously; it is also used in the trajectory ﬁle to label to the columns corresponding to this colvar. - width ⟨Colvar ﬂuctuation scale, or resolution for grid-based methods⟩

Context: colvar

Acceptable values: positive decimal

Default value: 1.0

Description: This number has the same physical unit as the colvar value and deﬁnes an eﬀective colvar unit. Harmonic restraints (7.4) use it to set the physical unit of the force constant, which is useful for multidimensional restraints involving variables with very diﬀerent units (for examples, Å or degrees^{∘}) with a single, scaled force constant. Histograms (7.9), ABF (7.1) and metadynamics (7.3) all use this number as the initial choice for the grid spacing along this variable: for this reason, width should generally be no larger than the standard deviation of the colvar in an unbiased simulation. Unless it is required to control the spacing, it is usually simplest to keep the default value of 1, so that restraint force constants are provided in more intuitive units. - lowerBoundary ⟨Lower boundary of the colvar⟩

Context: colvar

Acceptable values: decimal

Description: Deﬁnes the lowest end of the interval of “relevant” values for the colvar. This number can be either a true physical boundary, or a user-deﬁned number. Together with upperBoundary and width, it is used to deﬁne a grid of values along the colvar (not available for colvars based on distanceDir, distanceVec, and orientation). This option does not aﬀect dynamics: to conﬁne a colvar within a certain interval, use a harmonicWalls bias. - upperBoundary ⟨Upper boundary of the colvar⟩

Context: colvar

Acceptable values: decimal

Description: Similarly to lowerBoundary, deﬁnes the highest possible or allowed value. - hardLowerBoundary ⟨Whether the lower boundary is the physical lower limit⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: This option does not aﬀect simulation results, but enables some internal optimizations. Depending on its mathematical deﬁnition, a colvar may have “natural” boundaries: for example, a distance colvar has a “natural” lower boundary at 0. Setting this option instructs the Colvars module that the user-deﬁned lower boundary is “natural”. See Section 6 for the physical ranges of values of each component. - hardUpperBoundary ⟨Whether the upper boundary is the physical upper limit of the colvar’s
values⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: Analogous to hardLowerBoundary. - expandBoundaries ⟨Allow to expand the two boundaries if needed⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: If deﬁned, biasing and analysis methods may keep their own copies of lowerBoundary and upperBoundary, and expand them to accommodate values that do not ﬁt in the initial range. Currently, this option is used by the metadynamics bias (7.3) to keep all of its hills fully within the grid. This option cannot be used when the initial boundaries already span the full period of a periodic colvar. - subtractAppliedForce ⟨Do not include biasing forces in the total force for this colvar⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: If the colvar supports total force calculation (see 6.3.3), all forces applied to this colvar by biases will be removed from the total force. This keyword allows to recover some of the “system force” calculation available in the Colvars module before version 2016-08-10. Please note that removal of all other external forces (including biasing forces applied to a diﬀerent colvar) is no longer supported, due to changes in the underlying simulation engines (primarily NAMD). This option may be useful when continuing a previous simulation where the removal of external/applied forces is essential. For all new simulations, the use of this option is not recommended.

- outputValue ⟨Output a trajectory for this colvar⟩

Context: colvar

Acceptable values: boolean

Default value: on

Description: If colvarsTrajFrequency is non-zero, the value of this colvar is written to the trajectory ﬁle every colvarsTrajFrequency steps in the column labeled “<name>”. - outputVelocity ⟨Output a velocity trajectory for this colvar⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: If colvarsTrajFrequency is deﬁned, the ﬁnite-diﬀerence calculated velocity of this colvar are written to the trajectory ﬁle under the label “v_<name>”. - outputEnergy ⟨Output an energy trajectory for this colvar⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: This option applies only to extended Lagrangian colvars. If colvarsTrajFrequency is deﬁned, the kinetic energy of the extended degree and freedom and the potential energy of the restraining spring are are written to the trajectory ﬁle under the labels “Ek_<name>” and “Ep_<name>”. - outputTotalForce ⟨Output a total force trajectory for this colvar⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: If colvarsTrajFrequency is deﬁned, the total force on this colvar (i.e. the projection of all atomic total forces onto this colvar — see equation (19) in section 7.1) are written to the trajectory ﬁle under the label “fs_<name>”. For extended Lagrangian colvars, the “total force” felt by the extended degree of freedom is simply the force from the harmonic spring. Note: not all components support this option. The physical unit for this force is kcal/mol, divided by the colvar unit U. - outputAppliedForce ⟨Output an applied force trajectory for this colvar⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: If colvarsTrajFrequency is deﬁned, the total force applied on this colvar by Colvars biases are written to the trajectory under the label “fa_<name>”. For extended Lagrangian colvars, this force is actually applied to the extended degree of freedom rather than the geometric colvar itself. The physical unit for this force is kcal/mol divided by the colvar unit.

The following options enable extended-system dynamics, where a colvar is coupled to an additional degree of freedom (ﬁctitious particle) by a harmonic spring. All biasing and conﬁning forces are then applied to the extended degree of freedom. The “actual” geometric colvar (function of Cartesian coordinates) only feels the force from the harmonic spring. This is particularly useful when combined with an ABF bias (7.1) to perform eABF simulations (7.2).

- extendedLagrangian ⟨Add extended degree of freedom⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: Adds a ﬁctitious particle to be coupled to the colvar by a harmonic spring. The ﬁctitious mass and the force constant of the coupling potential are derived from the parameters extendedTimeConstant and extendedFluctuation, described below. Biasing forces on the colvar are applied to this ﬁctitious particle, rather than to the atoms directly. This implements the extended Lagrangian formalism used in some metadynamics simulations [2]. - extendedFluctuation ⟨Standard deviation between the colvar and the ﬁctitious particle (colvar
unit)⟩

Context: colvar

Acceptable values: positive decimal

Description: Deﬁnes the spring stiﬀness for the extendedLagrangian mode, by setting the typical deviation between the colvar and the extended degree of freedom due to thermal ﬂuctuation. The spring force constant is calculated internally as k_{B}T ∕σ^{2}, where σ is the value of extendedFluctuation. - extendedTimeConstant ⟨Oscillation period of the ﬁctitious particle (fs)⟩

Context: colvar

Acceptable values: positive decimal

Default value: 200

Description: Deﬁnes the inertial mass of the ﬁctitious particle, by setting the oscillation period of the harmonic oscillator formed by the ﬁctitious particle and the spring. The period should be much larger than the MD time step to ensure accurate integration of the extended particle’s equation of motion. The ﬁctitious mass is calculated internally as k_{B}T (τ∕2πσ)^{2}, where τ is the period and σ is the typical ﬂuctuation (see above). - extendedTemp ⟨Temperature for the extended degree of freedom (K)⟩

Context: colvar

Acceptable values: positive decimal

Default value: thermostat temperature

Description: Temperature used for calculating the coupling force constant of the extended variable (see extendedFluctuation) and, if needed, as a target temperature for extended Langevin dynamics (see extendedLangevinDamping). This should normally be left at its default value. - extendedLangevinDamping ⟨Damping factor for extended Langevin dynamics (ps
^{−1})⟩

Context: colvar

Acceptable values: positive decimal

Default value: 1.0

Description: If this is non-zero, the extended degree of freedom undergoes Langevin dynamics at temperature extendedTemp. The friction force is minus extendedLangevinDamping times the velocity. This is useful because the extended dynamics coordinate may heat up in the transient non-equilibrium regime of ABF. Use moderate damping values, to limit viscous friction (potentially slowing down diﬀusive sampling) and stochastic noise (increasing the variance of statistical measurements). In doubt, use the default value.

When the global keyword analysis is deﬁned in the conﬁguration ﬁle, run-time calculations of statistical properties for individual colvars can be performed. At the moment, several types of time correlation functions, running averages and running standard deviations are available.

- corrFunc ⟨Calculate a time correlation function?⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: Whether or not a time correlaction function should be calculated for this colvar. - corrFuncWithColvar ⟨Colvar name for the correlation function⟩

Context: colvar

Acceptable values: string

Description: By default, the auto-correlation function (ACF) of this colvar, ξ_{i}, is calculated. When this option is speciﬁed, the correlation function is calculated instead with another colvar, ξ_{j}, which must be of the same type (scalar, vector, or quaternion) as ξ_{i}. - corrFuncType ⟨Type of the correlation function⟩

Context: colvar

Acceptable values: velocity, coordinate or coordinate_p2

Default value: velocity

Description: With coordinate or velocity, the correlation function C_{i,j}(t) = is calculated between the variables ξ_{i}and ξ_{j}, or their velocities. Π(ξ_{i},ξ_{j}) is the scalar product when calculated between scalar or vector values, whereas for quaternions it is the cosine between the two corresponding rotation axes. With coordinate_p2, the second order Legendre polynomial, (3cos(𝜃)^{2}−1)∕2, is used instead of the cosine. - corrFuncNormalize ⟨Normalize the time correlation function?⟩

Context: colvar

Acceptable values: boolean

Default value: on

Description: If enabled, the value of the correlation function at t = 0 is normalized to 1; otherwise, it equals to . - corrFuncLength ⟨Length of the time correlation function⟩

Context: colvar

Acceptable values: positive integer

Default value: 1000

Description: Length (in number of points) of the time correlation function. - corrFuncStride ⟨Stride of the time correlation function⟩

Context: colvar

Acceptable values: positive integer

Default value: 1

Description: Number of steps between two values of the time correlation function. - corrFuncOffset ⟨Oﬀset of the time correlation function⟩

Context: colvar

Acceptable values: positive integer

Default value: 0

Description: The starting time (in number of steps) of the time correlation function (default: t = 0). Note: the value at t = 0 is always used for the normalization. - corrFuncOutputFile ⟨Output ﬁle for the time correlation function⟩

Context: colvar

Acceptable values: UNIX ﬁlename

Default value: <name>.corrfunc.dat

Description: The time correlation function is saved in this ﬁle. - runAve ⟨Calculate the running average and standard deviation⟩

Context: colvar

Acceptable values: boolean

Default value: off

Description: Whether or not the running average and standard deviation should be calculated for this colvar. - runAveLength ⟨Length of the running average window⟩

Context: colvar

Acceptable values: positive integer

Default value: 1000

Description: Length (in number of points) of the running average window. - runAveStride ⟨Stride of the running average window values⟩

Context: colvar

Acceptable values: positive integer

Default value: 1

Description: Number of steps between two values within the running average window. - runAveOutputFile ⟨Output ﬁle for the running average and standard deviation⟩

Context: colvar

Acceptable values: UNIX ﬁlename

Default value: <name>.runave.dat

Description: The running average and standard deviation are saved in this ﬁle.

To deﬁne collective variables, atoms are usually selected as groups. Each group is deﬁned using an identiﬁer that is unique in the context of the speciﬁc colvar component (e.g. for a distance component, the two groups are group1 and group2). The identiﬁer is followed by a brace-delimited block containing selection keywords and other parameters, including an optional name:

- name ⟨Unique name for the atom group⟩

Context: atom group

Acceptable values: string

Description: This parameter deﬁnes a unique name for this atom group, which can be referred to in the deﬁnition of other atom groups (including in other colvars) by invoking atomsOfGroup as a selection keyword.

Selection keywords may be used individually or in combination with each other, and each can be repeated any
number of times. Selection is incremental: each keyword adds the corresponding atoms to the selection, so that
diﬀerent sets of atoms can be combined. However, atoms included by multiple keywords are only counted once.
Below is an example conﬁguration for an atom group called “atoms”. Note: this is an unusually varied combination
of selection keywords, demonstrating how they can be combined together: most simulations only use one of
them.

atoms {

# add atoms 1 and 3 to this group (note: the first atom in the system is 1)

atomNumbers {

1 3

}

# add atoms starting from 20 up to and including 50

atomNumbersRange 20-50

# add all the atoms with occupancy 2 in the file atoms.pdb

atomsFile atoms.pdb

atomsCol O

atomsColValue 2.0

# add all the C-alphas within residues 11 to 20 of segments "PR1" and "PR2"

psfSegID PR1 PR2

atomNameResidueRange CA 11-20

atomNameResidueRange CA 11-20

# add index group (requires a .ndx file to be provided globally)

indexGroup Water

}

The resulting selection includes atoms 1 and 3, those between 20 and 50, the C_{α} atoms between residues 11 and
20 of the two segments PR1 and PR2, and those in the index group called “Water”. The indices of this group are read
from the ﬁle provided by the global keyword indexFile.

In the current version, the Colvars module does not manipulate VMD atom selections directly: however, these can be converted to atom groups within the Colvars conﬁguration string, using selection keywords such as atomNumbers. The complete list of selection keywords available in VMD is:

- atomNumbers ⟨List of atom numbers⟩

Context: atom group

Acceptable values: space-separated list of positive integers

Description: This option adds to the group all the atoms whose numbers are in the list. The number of the ﬁrst atom in the system is 1: to convert from a VMD selection, use “atomselect get serial”. - indexGroup ⟨Name of index group to be used (GROMACS format)⟩

Context: atom group

Acceptable values: string

Description: If the name of an index ﬁle has been provided by indexFile, this option allows to select one index group from that ﬁle: the atoms from that index group will be used to deﬁne the current group. - atomsOfGroup ⟨Name of group deﬁned previously⟩

Context: atom group

Acceptable values: string

Description: Refers to a group deﬁned previously using its user-deﬁned name. This adds all atoms of that named group to the current group. - atomNumbersRange ⟨Atoms within a number range⟩

Context: atom group

Acceptable values: <Starting number>-<Ending number>

Description: This option includes in the group all atoms whose numbers are within the range speciﬁed. The number of the ﬁrst atom in the system is 1. - atomNameResidueRange ⟨Named atoms within a range of residue numbers⟩

Context: atom group

Acceptable values: <Atom name> <Starting residue>-<Ending residue>

Description: This option adds to the group all the atoms with the provided name, within residues in the given range. - psfSegID ⟨PSF segment identiﬁer⟩

Context: atom group

Acceptable values: space-separated list of strings (max 4 characters)

Description: This option sets the PSF segment identiﬁer for atomNameResidueRange. Multiple values may be provided, which correspond to multiple instances of atomNameResidueRange, in order of their occurrence. This option is only necessary if a PSF topology ﬁle is used. - atomsFile ⟨PDB ﬁle name for atom selection⟩

Context: atom group

Acceptable values: UNIX ﬁlename

Description: This option selects atoms from the PDB ﬁle provided and adds them to the group according to numerical ﬂags in the column atomsCol. Note: the sequence of atoms in the PDB ﬁle provided must match that in the system’s topology. - atomsCol ⟨PDB column to use for atom selection ﬂags⟩

Context: atom group

Acceptable values: O, B, X, Y, or Z

Description: This option speciﬁes which PDB column in atomsFile is used to determine which atoms are to be included in the group. - atomsColValue ⟨Atom selection ﬂag in the PDB column⟩

Context: atom group

Acceptable values: positive decimal

Description: If deﬁned, this value in atomsCol identiﬁes atoms in atomsFile that are included in the group. If undeﬁned, all atoms with a non-zero value in atomsCol are included. - dummyAtom ⟨Dummy atom position (Å)⟩

Context: atom group

Acceptable values: (x, y, z) triplet

Description: Instead of selecting any atom, this option makes the group a virtual particle at a ﬁxed position in space. This is useful e.g. to replace a group’s center of geometry with a user-deﬁned position.

The following options deﬁne an automatic calculation of an optimal translation (centerReference) or optimal
rotation (rotateReference), that superimposes the positions of this group to a provided set of reference
coordinates. This can allow, for example, to eﬀectively remove from certain colvars the eﬀects of
molecular tumbling and of diﬀusion. Given the set of atomic positions x_{i}, the colvar ξ can be deﬁned
on a set of roto-translated positions x_{i}′ = R(x_{i} − x^{C})+ x^{ref}. x^{C} is the geometric center of the x_{i}, R is
the optimal rotation matrix to the reference positions and x^{ref} is the geometric center of the reference
positions.

Components that are deﬁned based on pairwise distances are naturally invariant under global roto-translations. Other components are instead aﬀected by global rotations or translations: however, they can be made invariant if they are expressed in the frame of reference of a chosen group of atoms, using the centerReference and rotateReference options. Finally, a few components are deﬁned by convention using a roto-translated frame (e.g. the minimal RMSD): for these components, centerReference and rotateReference are enabled by default. In typical applications, the default settings result in the expected behavior.

Note that centerReference and rotateReference may aﬀect the Jacobian derivative of colvar components in a way that is not taken into account by default. Be careful when using these options in ABF simulations or when using total force values. At this point, only the RMSD component will correctly adjust the Jacobian derivative computation to all situations.

- centerReference ⟨Implicitly remove translations for this group⟩

Context: atom group

Acceptable values: boolean

Default value: off

Description: If this option is on, the center of geometry of the group will be aligned with that of the reference positions provided by either refPositions or refPositionsFile. Colvar components will only have access to the aligned positions. Note: unless otherwise speciﬁed, rmsd and eigenvector set this option to on by default. - rotateReference ⟨Implicitly remove rotations for this group⟩

Context: atom group

Acceptable values: boolean

Default value: off

Description: If this option is on, the coordinates of this group will be optimally superimposed to the reference positions provided by either refPositions or refPositionsFile. The rotation will be performed around the center of geometry if centerReference is on, or around the origin otherwise. The algorithm used is the same employed by the orientation colvar component [3]. Forces applied to the atoms of this group will also be implicitly rotated back to the original frame. Note: unless otherwise speciﬁed, rmsd and eigenvector set this option to on by default. - refPositions ⟨Reference positions for ﬁtting (Å)⟩

Context: atom group

Acceptable values: space-separated list of (x, y, z) triplets

Description: This option provides a list of reference coordinates for centerReference and/or rotateReference, and is mutually exclusive with refPositionsFile. If only centerReference is on, the list may contain a single (x, y, z) triplet; if also rotateReference is on, the list should be as long as the atom group, and its order must match the order in which atoms were deﬁned. - refPositionsFile ⟨File containing the reference positions for ﬁtting⟩

Context: atom group

Acceptable values: UNIX ﬁlename

Description: This option provides a list of reference coordinates for centerReference and/or rotateReference, and is mutually exclusive with refPositions. The acceptable ﬁle format is XYZ, which is read in double precision, or PDB; the latter is discouraged if the precision of the reference coordinates is a concern. Atomic positions are read diﬀerently depending on the following scenarios: (i) the ﬁle contains exactly as many records as the atoms in the group: all positions are read in sequence; (ii) (most common case) the ﬁle contains coordinates for the entire system: only the positions corresponding to the numeric indices of the atom group are read; (iii) if the ﬁle is a PDB ﬁle and refPositionsCol is speciﬁed, positions are read according to the value of the column refPositionsCol (which may be the same as atomsCol). In each case, atoms are read from the ﬁle in order of increasing number. - refPositionsCol ⟨PDB column containing atom ﬂags⟩

Context: atom group

Acceptable values: O, B, X, Y, or Z

Description: Like atomsCol for atomsFile, indicates which column to use to identify the atoms in refPositionsFile (if this is a PDB ﬁle). - refPositionsColValue ⟨Atom selection ﬂag in the PDB column⟩

Context: atom group

Acceptable values: positive decimal

Description: Analogous to atomsColValue, but applied to refPositionsCol. - fittingGroup ⟨Use an alternate set of atoms to deﬁne the roto-translation⟩

Context: atom group

Acceptable values: Block fittingGroup { ... }

Default value: This group itself

Description: If either centerReference or rotateReference is deﬁned, this keyword deﬁnes an alternate atom group to calculate the optimal roto-translation. Use this option to deﬁne a continuous rotation if the structure of the group involved changes signiﬁcantly (a typical symptom would be the message “Warning: discontinuous rotation!”).The following example illustrates the syntax of fittingGroup: a group called “atoms” is deﬁned, including 8 C

_{α}atoms of a protein of 100 residues. An optimal roto-translation is calculated automatically by ﬁtting the C_{α}trace of the rest of the protein onto the coordinates provided by a PDB ﬁle.# Example: defining a group "atoms", with its coordinates expressed

# on a roto-translated frame of reference defined by a second group

atoms {

psfSegID PROT

atomNameResidueRange CA 41-48

centerReference yes

rotateReference yes

fittingGroup {

# define the frame by fitting the rest of the protein

psfSegID PROT PROT

atomNameResidueRange CA 1-40

atomNameResidueRange CA 49-100

}

refPositionsFile all.pdb # can be the entire system

}

The following two options have default values appropriate for the vast majority of applications, and are only provided to support rare, special cases.

- enableFitGradients ⟨Include the roto-translational contribution to colvar gradients⟩

Context: atom group

Acceptable values: boolean

Default value: on

Description: When either centerReference or rotateReference is on, the gradients of some colvars include terms proportional to ∂R∕∂x_{i}(rotational gradients) and ∂x^{C}∕∂x_{i}(translational gradients). By default, these terms are calculated and included in the total gradients; if this option is set to off, they are neglected. In the case of a minimum RMSD component, this ﬂag is automatically disabled because the contributions of those derivatives to the gradients cancel out. - enableForces ⟨Apply forces from this colvar to this group⟩

Context: atom group

Acceptable values: boolean

Default value: on

Description: If this option is off, no forces are applied the atoms in the group. Other forces are not aﬀected (i.e. those from the MD engine, from other colvars, and other external forces). For dummy atoms, this option is off by default.

When periodic boundary conditions are deﬁned, the Colvars module requires that the coordinates of each molecular fragment are contiguous, without “jumps” when a fragment is partially wrapped near a periodic boundary. The Colvars module relies on this assumption when calculating a group’s center of geometry, but the condition may fail if the group spans diﬀerent molecules. In general, coordinate wrapping does not aﬀect the calculation of colvars if each atom group satisﬁes one or more of the following:

- it is composed by only one atom;
- it is used by a colvar component which does not make use of its center of geometry, but only of pairwise distances (distanceInv, coordNum, hBond, alpha, dihedralPC);
- it is used by a colvar component that ignores the ill-deﬁned Cartesian components of its center of mass (such as the x and y components of a membrane’s center of mass modeled with distanceZ).

If none of these conditions are met, wrapping may aﬀect the calculation of collective variables: a possible solution is to use pbc wrap or pbc unwrap prior to processing a trajectory with the Colvars module.

In simulations performed with message-passing programs (such as NAMD or LAMMPS), the calculation of energy and forces is distributed (i.e., parallelized) across multiple nodes, as well as over the processor cores of each node. When Colvars is enabled, certain atomic coordinates are collected on a single node, where the calculation of collective variables and of their biases is executed. This means that for simulations over large numbers of nodes, a Colvars calculation may produce a signiﬁcant overhead, coming from the costs of transmitting atomic coordinates to one node and of processing them.

Performance can be improved in multiple ways:

- The calculation of variables, components and biases can be distributed over the processor cores of the node where the Colvars module is executed. Currently, an equal weight is assigned to each colvar, or to each component of those colvars that include more than one component. The performance of simulations that use many colvars or components is improved automatically. For simulations that use a single large colvar, it may be advisable to partition it in multiple components, which will be then distributed across the available cores. If printed, the message “SMP parallelism is available.” indicates the availability of the option (will be supported in a future relase of VMD). If available, the option is turned on by default, but may be disabled using the keyword smp if required for debugging.
- As a general rule, the size of atom groups should be kept relatively small (up to a few thousands of atoms, depending on the size of the entire system in comparison). To gain an estimate of the computational cost of a large colvar, one can use a test calculation of the same colvar in VMD (hint: use the time Tcl command to measure the cost of running cv update).

In this context, the function that computes a colvar is here called a component. A component’s choice and deﬁnition consists of a keyword indicating the type of function (e.g. rmsd), followed by a deﬁnition block specifying the atoms involved (see 5) and any additional parameters (cutoﬀs, “reference” values, …). At least one component must be chosen: if none of the keywords listed below is found, an error is raised.

Most components return a scalar value (i.e. a real number):

- distance: distance between two groups;
- distanceZ: projection of a distance vector on an axis;
- distanceXY: projection of a distance vector on a plane;
- distanceInv: mean distance between two groups of atoms (e.g. NOE-based distance);
- angle: angle between three groups;
- dihedral: torsional (dihedral) angle between four groups;
- dipoleAngle: angle between two groups and dipole of a third group;
- polarTheta: polar angle of a group in spherical coordinates;
- polarPhi: azimuthal angle of a group in spherical coordinates;
- coordNum: coordination number between two groups;
- selfCoordNum: coordination number of atoms within a group;
- hBond: hydrogen bond between two atoms;
- rmsd: root mean square deviation (RMSD) from a set of reference coordinates;
- eigenvector: projection of the atomic coordinates on a vector;
- orientationAngle: angle of the best-ﬁt rotation from a set of reference coordinates;
- orientationProj: cosine of orientationProj;
- spinAngle: projection orthogonal to an axis of the best-ﬁt rotation from a set of reference coordinates;
- tilt: projection on an axis of the best-ﬁt rotation from a set of reference coordinates;
- gyration: radius of gyration of a group of atoms;
- inertia: moment of inertia of a group of atoms;
- inertiaZ: moment of inertia of a group of atoms around a chosen axis;
- alpha: α-helix content of a protein segment.
- dihedralPC: projection of protein backbone dihedrals onto a dihedral principal component.

Some components do not return scalar, but vector values:

- distanceVec: distance vector between two groups (length: 3);
- distanceDir: unit vector parallel to distanceVec (length: 3);
- cartesian: vector of atomic Cartesian coordinates (length: N);
- distancePairs: vector of mutual distances (length: N
_{1}×N_{2}); - orientation: best-ﬁt rotation, expressed as a unit quaternion (length: 4).

The types of components used in a colvar (scalar or not) determine the properties of that colvar, and particularly which biasing or analysis methods can be applied.

What if “X” is not listed? If a function type is not available on this list, it may be possible to deﬁne it as a polynomial superposition of existing ones (see 6.4), or a scripted function (see 6.5).

In this section, all available component types are listed, along with their physical units and the ranges of values, if limited. Such limiting values can be used to deﬁne lowerBoundary and upperBoundary in the parent colvar.

For each type of component, the available conﬁgurations keywords are listed: when two components share certain keywords, the second component references to the documentation of the ﬁrst one that uses that keyword. The very few keywords that are available for all types of components are listed in a separate section 6.2.

The distance {...} block deﬁnes a distance component between the two atom groups, group1 and group2.

List of keywords (see also 6.4 for additional options):

- group1 ⟨First group of atoms⟩

Context: distance

Acceptable values: Block group1 {...}

Description: First group of atoms. - group2: analogous to group1
- forceNoPBC ⟨Calculate absolute rather than minimum-image distance?⟩

Context: distance

Acceptable values: boolean

Default value: no

Description: By default, in calculations with periodic boundary conditions, the distance component returns the distance according to the minimum-image convention. If this parameter is set to yes, PBC will be ignored and the distance between the coordinates as maintained internally will be used. This is only useful in a limited number of special cases, e.g. to describe the distance between remote points of a single macromolecule, which cannot be split across periodic cell boundaries, and for which the minimum-image distance might give the wrong result because of a relatively small periodic cell. - oneSiteTotalForce ⟨Measure total force on group 1 only?⟩

Context: angle, dipoleAngle, dihedral

Acceptable values: boolean

Default value: no

Description: If this is set to yes, the total force is measured along a vector ﬁeld (see equation (19) in section 7.1) that only involves atoms of group1. This option is only useful for ABF, or custom biases that compute total forces. See section 7.1 for details.

The value returned is a positive number (in Å), ranging from 0 to the largest possible interatomic distance within the chosen boundary conditions (with PBCs, the minimum image convention is used unless the forceNoPBC option is set).

The distanceZ {...} block deﬁnes a distance projection component, which can be seen as measuring the distance between two groups projected onto an axis, or the position of a group along such an axis. The axis can be deﬁned using either one reference group and a constant vector, or dynamically based on two reference groups. One of the groups can be set to a dummy atom to allow the use of an absolute Cartesian coordinate.

List of keywords (see also 6.4 for additional options):

- main ⟨Main group of atoms⟩

Context: distanceZ

Acceptable values: Block main {...}

Description: Group of atoms whose position r is measured. - ref ⟨Reference group of atoms⟩

Context: distanceZ

Acceptable values: Block ref {...}

Description: Reference group of atoms. The position of its center of mass is noted r_{1}below. - ref2 ⟨Secondary reference group⟩

Context: distanceZ

Acceptable values: Block ref2 {...}

Default value: none

Description: Optional group of reference atoms, whose position r_{2}can be used to deﬁne a dynamic projection axis: e = (∥r_{2}−r_{1}∥)^{−1}×(r_{2}−r_{1}). In this case, the origin is r_{m}= 1∕2(r_{1}+r_{2}), and the value of the component is e⋅(r−r_{m}). - axis ⟨Projection axis (Å)⟩

Context: distanceZ

Acceptable values: (x, y, z) triplet

Default value: (0.0, 0.0, 1.0)

Description: The three components of this vector deﬁne a projection axis e for the distance vector r−r_{1}joining the centers of groups ref and main. The value of the component is then e⋅(r−r_{1}). The vector should be written as three components separated by commas and enclosed in parentheses. - forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)

This component returns a number (in Å) whose range is determined by the chosen boundary conditions.
For instance, if the z axis is used in a simulation with periodic boundaries, the returned value ranges
between −b_{z}∕2 and b_{z}∕2, where b_{z} is the box length along z (this behavior is disabled if forceNoPBC is
set).

The distanceXY {...} block deﬁnes a distance projected on a plane, and accepts the same keywords as the component distanceZ, i.e. main, ref, either ref2 or axis, and oneSiteTotalForce. It returns the norm of the projection of the distance vector between main and ref onto the plane orthogonal to the axis. The axis is deﬁned using the axis parameter or as the vector joining ref and ref2 (see distanceZ above).

List of keywords (see also 6.4 for additional options):

- main: see deﬁnition of main in sec. 6.1.2 (distanceZ component)
- ref: see deﬁnition of ref in sec. 6.1.2 (distanceZ component)
- ref2: see deﬁnition of ref2 in sec. 6.1.2 (distanceZ component)
- axis: see deﬁnition of axis in sec. 6.1.2 (distanceZ component)
- forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)

The distanceVec {...} block deﬁnes a distance vector component, which accepts the same keywords as the component distance: group1, group2, and forceNoPBC. Its value is the 3-vector joining the centers of mass of group1 and group2.

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)

The distanceDir {...} block deﬁnes a distance unit vector component, which accepts the same keywords as
the component distance: group1, group2, and forceNoPBC. It returns a 3-dimensional unit vector d = (d_{x},d_{y},d_{z}),
with |d| = 1.

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)

The distanceInv {...} block deﬁnes a generalized mean distance between two groups of atoms 1 and 2, weighted with exponent 1∕n:

| (2) |

where ∥d^{ij}∥ is the distance between atoms i and j in groups 1 and 2 respectively, and n is an even
integer.

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)
- exponent ⟨Exponent n in equation 2⟩

Context: distanceInv

Acceptable values: positive even integer

Default value: 6

Description: Deﬁnes the exponent to which the individual distances are elevated before averaging. The default value of 6 is useful for example to applying restraints based on NOE-measured distances.

This component returns a number in Å, ranging from 0 to the largest possible distance within the chosen boundary conditions.

The distancePairs {...} block deﬁnes a N_{1} ×N_{2}-dimensional variable that includes all mutual distances
between the atoms of two groups. This can be useful, for example, to develop a new variable deﬁned over two
groups, by using the scriptedFunction feature.

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)

This component returns a N_{1} ×N_{2}-dimensional vector of numbers, each ranging from 0 to the largest possible distance
within the chosen boundary conditions.

The cartesian {...} block deﬁnes a component returning a ﬂat vector containing the Cartesian coordinates
of all participating atoms, in the order (x_{1},y_{1},z_{1},,x_{n},y_{n},z_{n}).

List of keywords (see also 6.4 for additional options):

- atoms ⟨Group of atoms⟩

Context: cartesian

Acceptable values: Block atoms {...}

Description: Deﬁnes the atoms whose coordinates make up the value of the component. If rotateReference or centerReference are deﬁned, coordinates are evaluated within the moving frame of reference.

The angle {...} block deﬁnes an angle, and contains the three blocks group1, group2 and group3, deﬁning the three groups. It returns an angle (in degrees) within the interval [0 : 180].

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- group3: analogous to group1
- forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)

The dipoleAngle {...} block deﬁnes an angle, and contains the three blocks group1, group2 and group3, deﬁning the three groups, being group1 the group where dipole is calculated. It returns an angle (in degrees) within the interval [0 : 180].

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- group3: analogous to group1
- forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)

The dihedral {...} block deﬁnes a torsional angle, and contains the blocks group1, group2, group3 and group4, deﬁning the four groups. It returns an angle (in degrees) within the interval [−180 : 180]. The Colvars module calculates all the distances between two angles taking into account periodicity. For instance, reference values for restraints or range boundaries can be deﬁned by using any real number of choice.

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- group3: analogous to group1
- group4: analogous to group1
- forceNoPBC: see deﬁnition of forceNoPBC in sec. 6.1.1 (distance component)
- oneSiteTotalForce: see deﬁnition of oneSiteTotalForce in sec. 6.1.1 (distance component)

The polarTheta {...} block deﬁnes the polar angle in spherical coordinates, for the center of mass of a group of atoms described by the block atoms. It returns an angle (in degrees) within the interval [0 : 180]. To obtain spherical coordinates in a frame of reference tied to another group of atoms, use the fittingGroup5.2 option within the atoms block.

List of keywords (see also 6.4 for additional options):

- atoms ⟨Atom group⟩

Context: polarPhi

Acceptable values: atoms {...} block

Description: Deﬁnes the group of atoms for the COM of which the angle should be calculated.

The polarPhi {...} block deﬁnes the azimuthal angle in spherical coordinates, for the center of mass of a group of atoms described by the block atoms. It returns an angle (in degrees) within the interval [−180 : 180]. The Colvars module calculates all the distances between two angles taking into account periodicity. For instance, reference values for restraints or range boundaries can be deﬁned by using any real number of choice.

List of keywords (see also 6.4 for additional options):

- atoms ⟨Atom group⟩

Context: polarPhi

Acceptable values: atoms {...} block

Description: Deﬁnes the group of atoms for the COM of which the angle should be calculated.

The coordNum {...} block deﬁnes a coordination number (or number of contacts), which calculates the
function (1−(d∕d_{0})^{n})∕(1−(d∕d_{0})^{m}), where d_{0} is the “cutoﬀ” distance, and n and m are exponents that can control
its long range behavior and stiﬀness [2]. This function is summed over all pairs of atoms in group1 and
group2:

| (3) |

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.1 (distance component)
- group2: analogous to group1
- cutoff ⟨“Interaction” distance (Å)⟩

Context: coordNum

Acceptable values: positive decimal

Default value: 4.0

Description: This number deﬁnes the switching distance to deﬁne an interatomic contact: for d ≪d_{0}, the switching function (1−(d∕d_{0})^{n})∕(1−(d∕d_{0})^{m}) is close to 1, at d = d_{0}it has a value of n∕m (1∕2 with the default n and m), and at d ≫ d_{0}it goes to zero approximately like d^{m−n}. Hence, for a proper behavior, m must be larger than n. - cutoff3 ⟨Reference distance vector (Å)⟩

Context: coordNum

Acceptable values: “(x, y, z)” triplet of positive decimals

Default value: (4.0, 4.0, 4.0)

Description: The three components of this vector deﬁne three diﬀerent cutoﬀs d_{0}for each direction. This option is mutually exclusive with cutoff. - expNumer ⟨Numerator exponent⟩

Context: coordNum

Acceptable values: positive even integer

Default value: 6

Description: This number deﬁnes the n exponent for the switching function. - expDenom ⟨Denominator exponent⟩

Context: coordNum

Acceptable values: positive even integer

Default value: 12

Description: This number deﬁnes the m exponent for the switching function. - group2CenterOnly ⟨Use only group2’s center of mass⟩

Context: coordNum

Acceptable values: boolean

Default value: off

Description: If this option is on, only contacts between each atoms in group1 and the center of mass of group2 are calculated (by default, the sum extends over all pairs of atoms in group1 and group2). If group2 is a dummyAtom, this option is set to yes by default. - tolerance ⟨Pairlist control⟩

Context: coordNum

Acceptable values: decimal

Default value: 0.0

Description: This controls the pairlist feature, dictating the minimum value for each summation element in Eq. 3 such that the pair that contributed the summation element is included in subsequent simulation timesteps until the next pairlist recalculation. For most applications, this value should be small (eg. 0.001) to avoid missing important contributions to the overall sum. Higher values will improve performance, although values above 1 will exclude all possible pair interactions. Similarly, values below 0 will never exclude a pair from consideration. - pairListFrequency ⟨Pairlist regeneration frequency⟩

Context: coordNum

Acceptable values: positive integer

Default value: 100

Description: This controls the pairlist feature, dictating how many steps are taken between regenerating pairlists if the tolerance is greater than 0. At this interval, the colvar deﬁned will be exact, as though it was the all-to-all pair summation deﬁned in Eq. 3. All other steps will report only values and gradients from pairs in the pairlist.

This component returns a dimensionless number, which ranges from approximately 0 (all interatomic distances
are much larger than the cutoﬀ) to N_{group1}×N_{group2} (all distances are less than the cutoﬀ), or N_{group1}
if group2CenterOnly is used. For performance reasons, at least one of group1 and group2 should
be of limited size or group2CenterOnly should be used: the cost of the loop over all pairs grows as
N_{group1}×N_{group2}.

The selfCoordNum {...} block deﬁnes a coordination number similarly to the component coordNum, but the function is summed over atom pairs within group1:

| (4) |

The keywords accepted by selfCoordNum are a subset of those accepted by coordNum, namely group1 (here deﬁning all of the atoms to be considered), cutoff, expNumer, and expDenom.

List of keywords (see also 6.4 for additional options):

- group1: see deﬁnition of group1 in sec. 6.1.14 (coordNum component)
- cutoff: see deﬁnition of cutoff in sec. 6.1.14 (coordNum component)
- cutoff3: see deﬁnition of cutoff3 in sec. 6.1.14 (coordNum component)
- expNumer: see deﬁnition of expNumer in sec. 6.1.14 (coordNum component)
- expDenom: see deﬁnition of expDenom in sec. 6.1.14 (coordNum component)
- tolerance: see deﬁnition of tolerance in sec. 6.1.14 (coordNum component)
- pairListFrequency: see deﬁnition of pairListFrequency in sec. 6.1.14 (coordNum component)

This component returns a dimensionless number, which ranges from approximately 0 (all interatomic
distances much larger than the cutoﬀ) to N_{group1}×(N_{group1}−1)∕2 (all distances within the cutoﬀ). For
performance reasons, group1 should be of limited size, because the cost of the loop over all pairs grows as
N_{group1}^{2}.

The hBond {...} block deﬁnes a hydrogen bond, implemented as a coordination number (eq. 3) between the donor and the acceptor atoms. Therefore, it accepts the same options cutoff (with a diﬀerent default value of 3.3 Å), expNumer (with a default value of 6) and expDenom (with a default value of 8). Unlike coordNum, it requires two atom numbers, acceptor and donor, to be deﬁned. It returns an adimensional number, with values between 0 (acceptor and donor far outside the cutoﬀ distance) and 1 (acceptor and donor much closer than the cutoﬀ).

List of keywords (see also 6.4 for additional options):

- acceptor ⟨Number of the acceptor atom⟩

Context: hBond

Acceptable values: positive integer

Description: Number that uses the same convention as atomNumbers. - donor: analogous to acceptor
- cutoff: see deﬁnition of cutoff in sec. 6.1.14 (coordNum component)

Note: default value is 3.3 Å. - expNumer: see deﬁnition of expNumer in sec. 6.1.14 (coordNum component)

Note: default value is 6. - expDenom: see deﬁnition of expDenom in sec. 6.1.14 (coordNum component)

Note: default value is 8.

The block rmsd {...} deﬁnes the root mean square replacement (RMSD) of a group of atoms with respect
to a reference structure. For each set of coordinates {x_{1}(t),x_{2}(t),…x_{N}(t)}, the colvar component rmsd
calculates the optimal rotation U^{{xi(t)}→{xi(ref)}} that best superimposes the coordinates {x_{i}(t)} onto a
set of reference coordinates {x_{i}^{(ref)}}. Both the current and the reference coordinates are centered on
their centers of geometry, x_{cog}(t) and x_{cog}^{(ref)}. The root mean square displacement is then deﬁned
as:

| (5) |

The optimal rotation U^{{xi(t)}→{xi(ref)}} is calculated within the formalism developed in reference [3], which
guarantees a continuous dependence of U^{{xi(t)}→{xi(ref)}} with respect to {x_{i}(t)}.

List of keywords (see also 6.4 for additional options):

- atoms ⟨Atom group⟩

Context: rmsd

Acceptable values: atoms {...} block

Description: Deﬁnes the group of atoms of which the RMSD should be calculated. Optimal ﬁt options (such as refPositions and rotateReference) should typically NOT be set within this block. Exceptions to this rule are the special cases discussed in the Advanced usage paragraph below. - refPositions ⟨Reference coordinates⟩

Context: rmsd

Acceptable values: space-separated list of (x, y, z) triplets

Description: This option (mutually exclusive with refPositionsFile) sets the reference coordinates for RMSD calculation, and uses these to compute the roto-translational ﬁt. It is functionally equivalent to the option refPositions in the atom group deﬁnition, which also supports more advanced ﬁtting options. - refPositionsFile ⟨Reference coordinates ﬁle⟩

Context: rmsd

Acceptable values: UNIX ﬁlename

Description: This option (mutually exclusive with refPositions) sets the reference coordinates for RMSD calculation, and uses these to compute the roto-translational ﬁt. It is functionally equivalent to the option refPositionsFile in the atom group deﬁnition, which also supports more advanced ﬁtting options. - refPositionsCol ⟨PDB column containing atom ﬂags⟩

Context: rmsd

Acceptable values: O, B, X, Y, or Z

Description: If refPositionsFile is a PDB ﬁle that contains all the atoms in the topology, this option may be provided to set which PDB ﬁeld is used to ﬂag the reference coordinates for atoms. - refPositionsColValue ⟨Atom selection ﬂag in the PDB column⟩

Context: rmsd

Acceptable values: positive decimal

Description: If deﬁned, this value identiﬁes in the PDB column refPositionsCol of the ﬁle refPositionsFile which atom positions are to be read. Otherwise, all positions with a non-zero value are read.

This component returns a positive real number (in Å).

In the standard usage as described above, the rmsd component calculates a minimum RMSD, that is, current coordinates are optimally ﬁtted onto the same reference coordinates that are used to compute the RMSD value. The ﬁt itself is handled by the atom group object, whose parameters are automatically set by the rmsd component. For very speciﬁc applications, however, it may be useful to control the ﬁtting process separately from the deﬁnition of the reference coordinates, to evaluate various types of non-minimal RMSD values. This can be achieved by setting the related options (refPositions, etc.) explicitly in the atom group block. This allows for the following non-standard cases:

- applying the optimal translation, but no rotation (rotateReference off), to bias or restrain the shape and orientation, but not the position of the atom group;
- applying the optimal rotation, but no translation (translateReference off), to bias or restrain the shape and position, but not the orientation of the atom group;
- disabling the application of optimal roto-translations, which lets the RMSD component decribe the deviation of atoms from ﬁxed positions in the laboratory frame: this allows for custom positional restraints within the Colvars module;
- ﬁtting the atomic positions to diﬀerent reference coordinates than those used in the RMSD calculation itself;
- applying the optimal rotation and/or translation from a separate atom group, deﬁned through fittingGroup: the RMSD then reﬂects the deviation from reference coordinates in a separate, moving reference frame.

The block eigenvector {...} deﬁnes the projection of the coordinates of a group of atoms (or more
precisely, their deviations from the reference coordinates) onto a vector in ℝ^{3n}, where n is the number of atoms in
the group. The computed quantity is the total projection:

| (6) |

where, as in the rmsd component, U is the optimal rotation matrix, x_{cog}(t) and x_{cog}^{(ref)} are the centers of geometry of
the current and reference positions respectively, and v_{i} are the components of the vector for each atom. Example
choices for (v_{i}) are an eigenvector of the covariance matrix (essential mode), or a normal mode of the system. It is
assumed that ∑_{i}v_{i} = 0: otherwise, the Colvars module centers the v_{i} automatically when reading them from the
conﬁguration.

List of keywords (see also 6.4 for additional options):

- atoms: see deﬁnition of atoms in sec. 6.1.17 (rmsd component)
- refPositions: see deﬁnition of refPositions in sec. 6.1.17 (rmsd component)
- refPositionsFile: see deﬁnition of refPositionsFile in sec. 6.1.17 (rmsd component)
- refPositionsCol: see deﬁnition of refPositionsCol in sec. 6.1.17 (rmsd component)
- refPositionsColValue: see deﬁnition of refPositionsColValue in sec. 6.1.17 (rmsd component)
- vector ⟨Vector components⟩

Context: eigenvector

Acceptable values: space-separated list of (x, y, z) triplets

Description: This option (mutually exclusive with vectorFile) sets the values of the vector components. - vectorFile ⟨ﬁle containing vector components⟩

Context: eigenvector

Acceptable values: UNIX ﬁlename

Description: This option (mutually exclusive with vector) sets the name of a coordinate ﬁle containing the vector components; the ﬁle is read according to the same format used for refPositionsFile. For a PDB ﬁle speciﬁcally, the components are read from the X, Y and Z ﬁelds. Note: The PDB ﬁle has limited precision and ﬁxed-point numbers: in some cases, the vector components may not be accurately represented; a XYZ ﬁle should be used instead, containing ﬂoating-point numbers. - vectorCol ⟨PDB column used to ﬂag participating atoms⟩

Context: eigenvector

Acceptable values: O or B

Description: Analogous to atomsCol. - vectorColValue ⟨Value used to ﬂag participating atoms in the PDB ﬁle⟩

Context: eigenvector

Acceptable values: positive decimal

Description: Analogous to atomsColValue. - differenceVector ⟨The 3n-dimensional vector is the diﬀerence between vector and
refPositions⟩

Context: eigenvector

Acceptable values: boolean

Default value: off

Description: If this option is on, the numbers provided by vector or vectorFile are interpreted as another set of positions, x_{i}′: the vector v_{i}is then deﬁned as v_{i}= . This allows to conveniently deﬁne a colvar ξ as a projection on the linear transformation between two sets of positions, “A” and “B”. For convenience, the vector is also normalized so that ξ = 0 when the atoms are at the set of positions “A” and ξ = 1 at the set of positions “B”.

This component returns a number (in Å), whose value ranges between the smallest and largest absolute positions in the unit cell during the simulations (see also distanceZ). Due to the normalization in eq. 6, this range does not depend on the number of atoms involved.

The block gyration {...} deﬁnes the parameters for calculating the radius of gyration of a group of atomic
positions {x_{1}(t),x_{2}(t),…x_{N}(t)} with respect to their center of geometry, x_{cog}(t):

| (7) |

This component must contain one atoms {...} block to deﬁne the atom group, and returns a positive number, expressed in Å.

List of keywords (see also 6.4 for additional options):

The block inertia {...} deﬁnes the parameters for calculating the total moment of inertia of a group of
atomic positions {x_{1}(t),x_{2}(t),…x_{N}(t)} with respect to their center of geometry, x_{cog}(t):

| (8) |

Note that all atomic masses are set to 1 for simplicity. This component must contain one atoms {...} block to
deﬁne the atom group, and returns a positive number, expressed in Å^{2}.

List of keywords (see also 6.4 for additional options):

The block inertiaZ {...} deﬁnes the parameters for calculating the component along the axis e of the
moment of inertia of a group of atomic positions {x_{1}(t),x_{2}(t),…x_{N}(t)} with respect to their center of geometry,
x_{cog}(t):

| (9) |

Note that all atomic masses are set to 1 for simplicity. This component must contain one atoms {...} block to
deﬁne the atom group, and returns a positive number, expressed in Å^{2}.

List of keywords (see also 6.4 for additional options):

- atoms: see deﬁnition of atoms in sec. 6.1.17 (rmsd component)
- axis ⟨Projection axis (Å)⟩

Context: inertiaZ

Acceptable values: (x, y, z) triplet

Default value: (0.0, 0.0, 1.0)

Description: The three components of this vector deﬁne (when normalized) the projection axis e.

The block orientation {...} returns the same optimal rotation used in the rmsd component to
superimpose the coordinates {x_{i}(t)} onto a set of reference coordinates {x_{i}^{(ref)}}. Such component returns a four
dimensional vector q = (q_{0},q_{1},q_{2},q_{3}), with ∑_{i}q_{i}^{2} = 1; this quaternion expresses the optimal rotation
{x_{i}(t)}→{x_{i}^{(ref)}} according to the formalism in reference [3]. The quaternion (q_{0},q_{1},q_{2},q_{3}) can also be written as
, where 𝜃 is the angle and u the normalized axis of rotation; for example, a rotation of 90^{∘}
around the z axis is expressed as “(0.707, 0.0, 0.0, 0.707)”. The script quaternion2rmatrix.tcl
provides Tcl functions for converting to and from a 4×4 rotation matrix in a format suitable for usage in
VMD.

As for the component rmsd, the available options are atoms, refPositionsFile, refPositionsCol and refPositionsColValue, and refPositions.

Note: refPositionsand refPositionsFile deﬁne the set of positions from which the optimal rotation is calculated, but this rotation is not applied to the coordinates of the atoms involved: it is used instead to deﬁne the variable itself.

List of keywords (see also 6.4 for additional options):

- atoms: see deﬁnition of atoms in sec. 6.1.17 (rmsd component)
- refPositions: see deﬁnition of refPositions in sec. 6.1.17 (rmsd component)
- refPositionsFile: see deﬁnition of refPositionsFile in sec. 6.1.17 (rmsd component)
- refPositionsCol: see deﬁnition of refPositionsCol in sec. 6.1.17 (rmsd component)
- refPositionsColValue: see deﬁnition of refPositionsColValue in sec. 6.1.17 (rmsd component)
- closestToQuaternion ⟨Reference rotation⟩

Context: orientation

Acceptable values: “(q0, q1, q2, q3)” quadruplet

Default value: (1.0, 0.0, 0.0, 0.0) (“null” rotation)

Description: Between the two equivalent quaternions (q_{0},q_{1},q_{2},q_{3}) and (−q_{0},−q_{1},−q_{2},−q_{3}), the closer to (1.0, 0.0, 0.0, 0.0) is chosen. This simpliﬁes the visualization of the colvar trajectory when samples values are a smaller subset of all possible rotations. Note: this only aﬀects the output, never the dynamics.

Tip: stopping the rotation of a protein. To stop the rotation of an elongated macromolecule in solution (and use an anisotropic box to save water molecules), it is possible to deﬁne a colvar with an orientation component, and restrain it throuh the harmonic bias around the identity rotation, (1.0, 0.0, 0.0, 0.0). Only the overall orientation of the macromolecule is aﬀected, and not its internal degrees of freedom. The user should also take care that the macromolecule is composed by a single chain, or disable wrapAll otherwise.

The block orientationAngle {...} accepts the same base options as the component orientation: atoms,
refPositions, refPositionsFile, refPositionsCol and refPositionsColValue. The returned value is the
angle of rotation 𝜃 between the current and the reference positions. This angle is expressed in degrees within the
range [0^{∘}:180^{∘}].

List of keywords (see also 6.4 for additional options):

- atoms: see deﬁnition of atoms in sec. 6.1.17 (rmsd component)
- refPositions: see deﬁnition of refPositions in sec. 6.1.17 (rmsd component)
- refPositionsFile: see deﬁnition of refPositionsFile in sec. 6.1.17 (rmsd component)
- refPositionsCol: see deﬁnition of refPositionsCol in sec. 6.1.17 (rmsd component)
- refPositionsColValue: see deﬁnition of refPositionsColValue in sec. 6.1.17 (rmsd component)

The block orientationProj {...} accepts the same base options as the component orientation: atoms, refPositions, refPositionsFile, refPositionsCol and refPositionsColValue. The returned value is the cosine of the angle of rotation 𝜃 between the current and the reference positions. The range of values is [-1:1].

List of keywords (see also 6.4 for additional options):

- atoms: see deﬁnition of atoms in sec. 6.1.17 (rmsd component)
- refPositions: see deﬁnition of refPositions in sec. 6.1.17 (rmsd component)
- refPositionsFile: see deﬁnition of refPositionsFile in sec. 6.1.17 (rmsd component)
- refPositionsCol: see deﬁnition of refPositionsCol in sec. 6.1.17 (rmsd component)
- refPositionsColValue: see deﬁnition of refPositionsColValue in sec. 6.1.17 (rmsd component)

The complete rotation described by orientation can optionally be decomposed into two sub-rotations: one is a “spin” rotation around e, and the other a “tilt” rotation around an axis orthogonal to e. The component spinAngle measures the angle of the “spin” sub-rotation around e.

List of keywords (see also 6.4 for additional options):

- atoms: see deﬁnition of atoms in sec. 6.1.17 (rmsd component)
- refPositions: see deﬁnition of refPositions in sec. 6.1.17 (rmsd component)
- refPositionsFile: see deﬁnition of refPositionsFile in sec. 6.1.17 (rmsd component)
- refPositionsCol: see deﬁnition of refPositionsCol in sec. 6.1.17 (rmsd component)
- refPositionsColValue: see deﬁnition of refPositionsColValue in sec. 6.1.17 (rmsd component)
- axis ⟨Special rotation axis (Å)⟩

Context: tilt

Acceptable values: (x, y, z) triplet

Default value: (0.0, 0.0, 1.0)

Description: The three components of this vector deﬁne (when normalized) the special rotation axis used to calculate the tilt and spinAngle components.

The component spinAngle returns an angle (in degrees) within the periodic interval [−180 : 180].

Note: the value of spinAngle is a continuous function almost everywhere, with the exception of conﬁgurations
with the corresponding “tilt” angle equal to 180^{∘} (i.e. the tilt component is equal to −1): in those cases,
spinAngle is undeﬁned. If such conﬁgurations are expected, consider deﬁning a tilt colvar using the same axis e,
and restraining it with a lower wall away from −1.

The component tilt measures the cosine of the angle of the “tilt” sub-rotation, which combined with the
“spin” sub-rotation provides the complete rotation of a group of atoms. The cosine of the tilt angle rather than the tilt
angle itself is implemented, because the latter is unevenly distributed even for an isotropic system: consider as an
analogy the angle 𝜃 in the spherical coordinate system. The component tilt relies on the same options as
spinAngle, including the deﬁnition of the axis e. The values of tilt are real numbers in the interval [−1 : 1]: the
value 1 represents an orientation fully parallel to e (tilt angle = 0^{∘}), and the value −1 represents an anti-parallel
orientation.

List of keywords (see also 6.4 for additional options):

- atoms: see deﬁnition of atoms in sec. 6.1.17 (rmsd component)
- refPositions: see deﬁnition of refPositions in sec. 6.1.17 (rmsd component)
- refPositionsFile: see deﬁnition of refPositionsFile in sec. 6.1.17 (rmsd component)
- refPositionsCol: see deﬁnition of refPositionsCol in sec. 6.1.17 (rmsd component)
- refPositionsColValue: see deﬁnition of refPositionsColValue in sec. 6.1.17 (rmsd component)
- axis: see deﬁnition of axis in sec. 6.1.26 (spinAngle component)

The block alpha {...} deﬁnes the parameters to calculate the helical content of a segment of protein
residues. The α-helical content across the N +1 residues N_{0} to N_{0} +N is calculated by the formula:

| (12) |

and the score function for the O^{(n)} ↔ N^{(n+4)} hydrogen bond is deﬁned through a hBond colvar component on the
same atoms.

List of keywords (see also 6.4 for additional options):

- residueRange ⟨Potential α-helical residues⟩

Context: alpha

Acceptable values: “<Initial residue number>-<Final residue number>”

Description: This option speciﬁes the range of residues on which this component should be deﬁned. The Colvars module looks for the atoms within these residues named “CA”, “N” and “O”, and raises an error if any of those atoms is not found. - psfSegID ⟨PSF segment identiﬁer⟩

Context: alpha

Acceptable values: string (max 4 characters)

Description: This option sets the PSF segment identiﬁer for the residues speciﬁed in residueRange. This option is only required when PSF topologies are used. - hBondCoeff ⟨Coeﬃcient for the hydrogen bond term⟩

Context: alpha

Acceptable values: positive between 0 and 1

Default value: 0.5

Description: This number speciﬁes the contribution to the total value from the hydrogen bond terms. 0 disables the hydrogen bond terms, 1 disables the angle terms. - angleRef ⟨Reference C
_{α}−C_{α}−C_{α}angle⟩

Context: alpha

Acceptable values: positive decimal

Default value: 88^{∘}

Description: This option sets the reference angle used in the score function (12). - angleTol ⟨Tolerance in the C
_{α}−C_{α}−C_{α}angle⟩

Context: alpha

Acceptable values: positive decimal

Default value: 15^{∘}

Description: This option sets the angle tolerance used in the score function (12). - hBondCutoff ⟨Hydrogen bond cutoﬀ⟩

Context: alpha

Acceptable values: positive decimal

Default value: 3.3 Å

Description: Equivalent to the cutoff option in the hBond component. - hBondExpNumer ⟨Hydrogen bond numerator exponent⟩

Context: alpha

Acceptable values: positive integer

Default value: 6

Description: Equivalent to the expNumer option in the hBond component. - hBondExpDenom ⟨Hydrogen bond denominator exponent⟩

Context: alpha

Acceptable values: positive integer

Default value: 8

Description: Equivalent to the expDenom option in the hBond component.

This component returns positive values, always comprised between 0 (lowest α-helical score) and 1 (highest α-helical score).

The block dihedralPC {...} deﬁnes the parameters to calculate the projection of backbone dihedral angles
within a protein segment onto a dihedral principal component, following the formalism of dihedral principal
component analysis (dPCA) proposed by Mu et al.[4] and documented in detail by Altis et al.[5]. Given a peptide or
protein segment of N residues, each with Ramachandran angles ϕ_{i} and ψ_{i}, dPCA rests on a variance/covariance
analysis of the 4(N −1) variables cos(ψ_{1}),sin(ψ_{1}),cos(ϕ_{2}),sin(ϕ_{2})cos(ϕ_{N}),sin(ϕ_{N}). Note that angles ϕ_{1} and
ψ_{N} have little impact on chain conformation, and are therefore discarded, following the implementation of dPCA in
the analysis software Carma.[6]

For a given principal component (eigenvector) of coeﬃcients (k_{i})_{1≤i≤4(N−1)}, the projection of the current
backbone conformation is:

| (13) |

dihedralPC expects the same parameters as the alpha component for deﬁning the relevant residues (residueRange and psfSegID) in addition to the following:

List of keywords (see also 6.4 for additional options):

- residueRange: see deﬁnition of residueRange in sec. 6.1.28 (alpha component)
- psfSegID: see deﬁnition of psfSegID in sec. 6.1.28 (alpha component)
- vectorFile ⟨File containing dihedral PCA eigenvector(s)⟩

Context: dihedralPC

Acceptable values: ﬁle name

Description: A text ﬁle containing the coeﬃcients of dihedral PCA eigenvectors on the cosine and sine coordinates. The vectors should be arranged in columns, as in the ﬁles output by Carma.[6] - vectorNumber ⟨File containing dihedralPCA eigenvector(s)⟩

Context: dihedralPC

Acceptable values: positive integer

Description: Number of the eigenvector to be used for this component.

The following options can be used for any of the above colvar components in order to obtain a polynomial combination or any user-supplied function provided by scriptedFunction.

- name ⟨Name of this component⟩

Context: any component

Acceptable values: string

Default value: type of component + numeric id

Description: The name is an unique case-sensitive string which allows the Colvars module to identify this component. This is useful, for example, when combining multiple components via a scriptedFunction. - scalable ⟨Attempt to calculate this component in parallel?⟩

Context: any component

Acceptable values: boolean

Default value: on, if available

Description: If set to on (default), the Colvars module will attempt to calculate this component in parallel to reduce overhead. Whether this option is available depends on the type of component: currently supported are distance, distanceZ, distanceXY, distanceVec, distanceDir, angle and dihedral. This ﬂag inﬂuences computational cost, but does not aﬀect numerical results: therefore, it should only be turned oﬀ for debugging or testing purposes.

The following components returns real numbers that lie in a periodic interval:

- dihedral: torsional angle between four groups;
- spinAngle: angle of rotation around a predeﬁned axis in the best-ﬁt from a set of reference coordinates.

In certain conditions, distanceZ can also be periodic, namely when periodic boundary conditions (PBCs) are deﬁned in the simulation and distanceZ’s axis is parallel to a unit cell vector.

The following keywords can be used within periodic components (and are illegal elsewhere):

- period ⟨Period of the component⟩

Context: distanceZ

Acceptable values: positive decimal

Default value: 0.0

Description: Setting this number enables the treatment of distanceZ as a periodic component: by default, distanceZ is not considered periodic. The keyword is supported, but irrelevant within dihedral or spinAngle, because their period is always 360 degrees. - wrapAround ⟨Center of the wrapping interval for periodic variables⟩

Context: distanceZ, dihedral or spinAngle

Acceptable values: decimal

Default value: 0.0

Description: By default, values of the periodic components are centered around zero, ranging from −P∕2 to P∕2, where P is the period. Setting this number centers the interval around this value. This can be useful for convenience of output, or to set the walls for a harmonicWalls in an order that would not otherwise be allowed.

Internally, all diﬀerences between two values of a periodic colvar follow the minimum image convention: they are calculated based on the two periodic images that are closest to each other.

Note: linear or polynomial combinations of periodic components (see 6.4) may become meaningless when components cross the periodic boundary. Use such combinations carefully: estimate the range of possible values of each component in a given simulation, and make use of wrapAround to limit this problem whenever possible.

When one of the following components are used, the deﬁned colvar returns a value that is not a scalar number:

- distanceVec: 3-dimensional vector of the distance between two groups;
- distanceDir: 3-dimensional unit vector of the distance between two groups;
- orientation: 4-dimensional unit quaternion representing the best-ﬁt rotation from a set of reference coordinates.

The distance between two 3-dimensional unit vectors is computed as the angle between them. The distance between two quaternions is computed as the angle between the two 4-dimensional unit vectors: because the orientation represented by q is the same as the one represented by −q, distances between two quaternions are computed considering the closest of the two symmetric images.

Non-scalar components carry the following restrictions:

- Calculation of total forces (outputTotalForce option) is currently not implemented.
- Each colvar can only contain one non-scalar component.
- Binning on a grid (abf, histogram and metadynamics with useGrids enabled) is currently not implemented for colvars based on such components.

Note: while these restrictions apply to individual colvars based on non-scalar components, no limit is set to the number of scalar colvars. To compute multi-dimensional histograms and PMFs, use sets of scalar colvars of arbitrary size.

In addition to the restrictions due to the type of value computed (scalar or non-scalar), a ﬁnal restriction can arise when calculating total force (outputTotalForce option or application of a abf bias). total forces are available currently only for the following components: distance, distanceZ, distanceXY, angle, dihedral, rmsd, eigenvector and gyration.

To extend the set of possible deﬁnitions of colvars ξ(r), multiple components q_{i}(r) can be summed with the
formula:

| (14) |

where each component appears with a unique coeﬃcient c_{i} (1.0 by default) the positive integer exponent n_{i} (1 by
default).

Any set of components can be combined within a colvar, provided that they return the same type of values (scalar, unit vector, vector, or quaternion). By default, the colvar is the sum of its components. Linear or polynomial combinations (following equation (14)) can be obtained by setting the following parameters, which are common to all components:

- componentCoeff ⟨Coeﬃcient of this component in the colvar⟩

Context: any component

Acceptable values: decimal

Default value: 1.0

Description: Deﬁnes the coeﬃcient by which this component is multiplied (after being raised to componentExp) before being added to the sum. - componentExp ⟨Exponent of this component in the colvar⟩

Context: any component

Acceptable values: integer

Default value: 1

Description: Deﬁnes the power at which the value of this component is raised before being added to the sum. When this exponent is diﬀerent than 1 (non-linear sum), total forces and the Jacobian force are not available, making the colvar unsuitable for ABF calculations.

Example: To deﬁne the average of a colvar across diﬀerent parts of the system, simply deﬁne within the same colvar block a series of components of the same type (applied to diﬀerent atom groups), and assign to each component a componentCoeff of 1∕N.

When scripting is supported (default in VMD), a colvar may be deﬁned as a scripted function of its components, rather than a linear or polynomial combination. When implementing generic functions of Cartesian coordinates rather than functions of existing components, the cartesian component may be particularly useful. A scalar-valued scripted variable may be manually deﬁned as periodic by providing the keyword period, and the optional keyword wrapAround, with the same meaning as in periodic components (see 6.3.1 for details).

An example of elaborate scripted colvar is given in example 10, in the form of path-based collective variables as deﬁned by Branduardi et al[7]. The required Tcl procedures are provided in the colvartools directory.

- scriptedFunction ⟨Compute colvar as a scripted function of its components⟩

Context: colvar

Acceptable values: string

Description: If this option is speciﬁed, the colvar will be computed as a scripted function of the values of its components. To that eﬀect, the user should deﬁne two Tcl procedures: calc_<scriptedFunction> and calc_<scriptedFunction>_gradient, both accepting as many parameters as the colvar has components. Values of the components will be passed to those procedures in the order deﬁned by their sorted name strings. Note that if all components are of the same type, their default names are sorted in the order in which they are deﬁned, so that names need only be speciﬁed for combinations of components of diﬀerent types. calc_<scriptedFunction> should return one value of type <scriptedFunctionType>, corresponding to the colvar value. calc_<scriptedFunction>_gradient should return a Tcl list containing the derivatives of the function with respect to each component. If both the function and some of the components are vectors, the gradient is really a Jacobian matrix that should be passed as a linear vector in row-major order, i.e. for a function f_{i}(x_{j}): ∇_{x}f_{1}∇_{x}f_{2}. - scriptedFunctionType ⟨Type of value returned by the scripted colvar⟩

Context: colvar

Acceptable values: string

Default value: scalar

Description: If a colvar is deﬁned as a scripted function, its type is not constrained by the types of its components. With this ﬂag, the user may specify whether the colvar is a scalar or one of the following vector types: vector3 (a 3D vector), unit_vector3 (a normalized 3D vector), or unit_quaternion (a normalized quaternion), or vector (a vector whose size is speciﬁed by scriptedFunctionVectorSize). Non-scalar values should be passed as space-separated lists. - scriptedFunctionVectorSize ⟨Dimension of the vector value of a scripted colvar⟩

Context: colvar

Acceptable values: positive integer

Description: This parameter is only valid when scriptedFunctionType is set to vector. It deﬁnes the vector length of the colvar value returned by the function.

All of the biasing and analysis methods implemented (abf, harmonic, histogram and metadynamics) recognize the following options:

- name ⟨Identiﬁer for the bias⟩

Context: colvar bias

Acceptable values: string

Default value: <type of bias><bias index>

Description: This string is used to identify the bias or analysis method in output messages and to name some output ﬁles. - colvars ⟨Collective variables involved⟩

Context: colvar bias

Acceptable values: space-separated list of colvar names

Description: This option selects by name all the colvars to which this bias or analysis will be applied. - outputEnergy ⟨Write the current bias energy to the trajectory ﬁle⟩

Context: colvar bias

Acceptable values: boolean

Default value: off

Description: If this option is chosen and colvarsTrajFrequency is not zero, the current value of the biasing energy will be written to the trajectory ﬁle during the simulation.

In addition, restraint biases (7.4, 7.6, 7.7, ...) and metadynamics biases (7.3) oﬀer the following optional keywords, which allow the use of thermodynamic integration (TI) to compute potentials of mean force (PMFs). In adaptive biasing force (ABF) biases (7.1) the same keywords are not recognized because their functionality is always included.

- writeTIPMF ⟨Write the PMF computed by thermodynamic integration⟩

Context: colvar bias

Acceptable values: boolean

Default value: off

Description: If the bias is applied to a variable that supports the calculation of total forces (see outputTotalForce and 6.3.3), this option allows calculating the corresponding PMF by thermodynanic integration, and writing it to the ﬁle outputName.<name>.ti.pmf, where <name> is the name of the bias. The total force includes the forces applied to the variable by all bias, except those from this bias itself. If any bias applies time-dependent forces besides the one using this option, an error is raised. - writeTISamples ⟨Write the free-energy gradient samples⟩

Context: colvar bias

Acceptable values: boolean

Default value: off

Description: This option allows to compute total forces for use with thermodynamic integration as done by the keyword writeTIPMF. The names of the ﬁles containing the variables’ histogram and mean thermodyunamic forces are outputName.<name>.ti.count and outputName.<name>.ti.grad, respectively: these can be used by abf_integrate or similar utility. This option on by default when writeTIPMF is on, but can be enabled separately if the bias is applied to more than one variable, making not possible the direct integration of the PMF at runtime. If any bias applies time-dependent forces besides the one using this option, an error is raised.

For a full description of the Adaptive Biasing Force method, see reference [8]. For details about this implementation, see references [9] and [10]. When publishing research that makes use of this functionality, please cite references [8] and [10].

An alternate usage of this feature is the application of custom tabulated biasing potentials to one or more colvars. See inputPrefix and updateBias below.

Combining ABF with the extended Lagrangian feature (4.3) of the variables produces the extended-system ABF variant of the method (7.2).

ABF is based on the thermodynamic integration (TI) scheme for computing free energy proﬁles. The free energy
as a function of a set of collective variables ξ = (ξ_{i})_{i∈[1,n]} is deﬁned from the canonical distribution of ξ ,
𝒫(ξ):

| (15) |

In the TI formalism, the free energy is obtained from its gradient, which is generally calculated in the form of
the average of a force F_{ξ} exerted on ξ , taken over an iso-ξ surface:

| (16) |

Several formulae that take the form of (16) have been proposed. This implementation relies partly on the classic
formulation [11], and partly on a more versatile scheme originating in a work by Ruiz-Montero et al. [12],
generalized by den Otter [13] and extended to multiple variables by Ciccotti et al. [14]. Consider a system subject
to constraints of the form σ_{k}(x) = 0. Let (v_{i})_{i∈[1,n]} be arbitrarily chosen vector ﬁelds (ℝ^{3N} → ℝ^{3N}) verifying, for all
i, j, and k:

then the following holds [14]:

| (19) |

where V is the potential energy function. v_{i} can be interpreted as the direction along which the force acting on
variable ξ_{i} is measured, whereas the second term in the average corresponds to the geometric entropy contribution
that appears as a Jacobian correction in the classic formalism [11]. Condition (17) states that the direction along
which the total force on ξ_{i} is measured is orthogonal to the gradient of ξ_{j}, which means that the force measured on
ξ_{i} does not act on ξ_{j}.

Equation (18) implies that constraint forces are orthogonal to the directions along which the free energy gradient is measured, so that the measurement is eﬀectively performed on unconstrained degrees of freedom.

In the framework of ABF, F_{ξ} is accumulated in bins of ﬁnite size δξ , thereby providing an estimate of the free
energy gradient according to equation (16). The biasing force applied along the collective variables to overcome
free energy barriers is calculated as:

| (20) |

where ∇_{x} denotes the current estimate of the free energy gradient at the current point ξ in the collective
variable subspace, and α(N_{ξ}) is a scaling factor that is ramped from 0 to 1 as the local number of samples N_{ξ}
increases to prevent nonequilibrium eﬀects in the early phase of the simulation, when the gradient estimate has a
large variance. See the fullSamples parameter below for details.

As sampling of the phase space proceeds, the estimate ∇_{x} is progressively reﬁned. The biasing force
introduced in the equations of motion guarantees that in the bin centered around ξ , the forces acting along the
selected collective variables average to zero over time. Eventually, as the undelying free energy surface is canceled
by the adaptive bias, evolution of the system along ξ is governed mainly by diﬀusion. Although this
implementation of ABF can in principle be used in arbitrary dimension, a higher-dimension collective variable
space is likely to result in sampling diﬃculties. Most commonly, the number of variables is one or
two.

The following conditions must be met for an ABF simulation to be possible and to produce an accurate estimate of the free energy proﬁle. Note that these requirements do not apply when using the extended-system ABF method (7.2).

- Only linear combinations of colvar components can be used in ABF calculations.
- Availability of total forces is necessary. The following colvar components can be used in ABF calculations: distance, distance_xy, distance_z, angle, dihedral, gyration, rmsd and eigenvector. Atom groups may not be replaced by dummy atoms, unless they are excluded from the force measurement by specifying oneSiteTotalForce, if available.
- Mutual orthogonality of colvars. In a multidimensional ABF calculation, equation (17) must be satisﬁed for
any two colvars ξ
_{i}and ξ_{j}. Various cases fulﬁll this orthogonality condition:- ξ
_{i}and ξ_{j}are based on non-overlapping sets of atoms. - atoms involved in the force measurement on ξ
_{i}do not participate in the deﬁnition of ξ_{j}. This can be obtained using the option oneSiteTotalForce of the distance, angle, and dihedral components (example: Ramachandran angles ϕ, ψ). - ξ
_{i}and ξ_{j}are orthogonal by construction. Useful cases are the sum and diﬀerence of two components, or distance_z and distance_xy using the same axis.

- ξ
- Mutual orthogonality of components: when several components are combined into a colvar, it is assumed that
their vectors v
_{i}(equation (19)) are mutually orthogonal. The cases described for colvars in the previous paragraph apply. - Orthogonality of colvars and constraints: equation 18 can be satisﬁed in two simple ways, if either no constrained atoms are involved in the force measurement (see point 3 above) or pairs of atoms joined by a constrained bond are part of an atom group which only intervenes through its center (center of mass or geometric center) in the force measurement. In the latter case, the contributions of the two atoms to the left-hand side of equation 18 cancel out. For example, all atoms of a rigid TIP3P water molecule can safely be included in an atom group used in a distance component.

ABF depends on parameters from collective variables to deﬁne the grid on which free energy gradients are computed. In the direction of each colvar, the grid ranges from lowerBoundary to upperBoundary, and the bin width (grid spacing) is set by the width parameter (see 4.1). The following speciﬁc parameters can be set in the ABF conﬁguration block:

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- fullSamples ⟨Number of samples in a bin prior to application of the ABF⟩

Context: abf

Acceptable values: positive integer

Default value: 200

Description: To avoid nonequilibrium eﬀects due to large ﬂuctuations of the force exerted along the colvars, it is recommended to apply a biasing force only after a the estimate has started converging. If fullSamples is non-zero, the applied biasing force is scaled by a factor α(N_{ξ}) between 0 and 1. If the number of samples N_{ξ}in the current bin is higher than fullSamples, the factor is one. If it is less than half of fullSamples, the factor is zero and no bias is applied. Between those two thresholds, the factor follows a linear ramp from 0 to 1: α(N_{ξ}) = (2N_{ξ}∕fullSamples)−1 . - maxForce ⟨Maximum magnitude of the ABF force⟩

Context: abf

Acceptable values: positive decimals (one per colvar)

Default value: disabled

Description: This option enforces a cap on the magnitude of the biasing force eﬀectively applied by this ABF bias on each colvar. This can be useful in the presence of singularities in the PMF such as hard walls, where the discretization of the average force becomes very inaccurate, causing the colvar’s diﬀusion to get “stuck” at the singularity. To enable this cap, provide one non-negative value for each colvar. The unit of force is kcal/mol divided by the colvar unit. - hideJacobian ⟨Remove geometric entropy term from calculated free energy gradient?⟩

Context: abf

Acceptable values: boolean

Default value: no

Description: In a few special cases, most notably distance-based variables, an alternate deﬁnition of the potential of mean force is traditionally used, which excludes the Jacobian term describing the eﬀect of geometric entropy on the distribution of the variable. This results, for example, in particle-particle potentials of mean force being ﬂat at large separations. Setting this parameter to yes causes the output data to follow that convention, by removing this contribution from the output gradients while applying internally the corresponding correction to ensure uniform sampling. It is not allowed for colvars with multiple components. - outputFreq ⟨Frequency (in timesteps) at which ABF data ﬁles are refreshed⟩

Context: abf

Acceptable values: positive integer

Default value: Colvars module restart frequency

Description: The ﬁles containing the free energy gradient estimate and sampling histogram (and the PMF in one-dimensional calculations) are written on disk at the given time interval. - historyFreq ⟨Frequency (in timesteps) at which ABF history ﬁles are accumulated⟩

Context: abf

Acceptable values: positive integer

Default value: 0

Description: If this number is non-zero, the free energy gradient estimate and sampling histogram (and the PMF in one-dimensional calculations) are appended to ﬁles on disk at the given time interval. History ﬁle names use the same preﬁx as output ﬁles, with “.hist” appended. - inputPrefix ⟨Filename preﬁx for reading ABF data⟩

Context: abf

Acceptable values: list of strings

Description: If this parameter is set, for each item in the list, ABF tries to read a gradient and a sampling ﬁles named <inputPrefix>.grad and <inputPrefix>.count. This is done at startup and sets the initial state of the ABF algorithm. The data from all provided ﬁles is combined appropriately. Also, the grid deﬁnition (min and max values, width) need not be the same that for the current run. This command is useful to piece together data from simulations in diﬀerent regions of collective variable space, or change the colvar boundary values and widths. Note that it is not recommended to use it to switch to a smaller width, as that will leave some bins empty in the ﬁner data grid. This option is NOT compatible with reading the data from a restart ﬁle (cv load command). - applyBias ⟨Apply the ABF bias?⟩

Context: abf

Acceptable values: boolean

Default value: yes

Description: If this is set to no, the calculation proceeds normally but the adaptive biasing force is not applied. Data is still collected to compute the free energy gradient. This is mostly intended for testing purposes, and should not be used in routine simulations. - updateBias ⟨Update the ABF bias?⟩

Context: abf

Acceptable values: boolean

Default value: yes

Description: If this is set to no, the initial biasing force (e.g. read from a restart ﬁle or through inputPrefix) is not updated during the simulation. As a result, a constant bias is applied. This can be used to apply a custom, tabulated biasing potential to any combination of colvars. To that eﬀect, one should prepare a gradient ﬁle containing the gradient of the potential to be applied (negative of the bias force), and a count ﬁle containing only values greater than fullSamples. These ﬁles must match the grid parameters of the colvars.

The ABF bias produces the following ﬁles, all in multicolumn text format:

- outputName.grad: current estimate of the free energy gradient (grid), in multicolumn;
- outputName.count: histogram of samples collected, on the same grid;
- outputName.pmf: only for one-dimensional calculations, integrated free energy proﬁle or PMF.

If several ABF biases are deﬁned concurrently, their name is inserted to produce unique ﬁlenames for output, as in outputName.abf1.grad. This should not be done routinely and could lead to meaningless results: only do it if you know what you are doing!

If the colvar space has been partitioned into sections (windows) in which independent ABF simulations have been run, the resulting data can be merged using the inputPrefix option described above (a run of 0 steps is enough).

If a one-dimensional calculation is performed, the estimated free energy gradient is automatically integrated and
a potential of mean force is written under the ﬁle name

In dimension 2 or greater, integrating the discretized gradient becomes non-trivial. The standalone utility abf_integrate is provided to perform that task. abf_integrate reads the gradient data and uses it to perform a Monte-Carlo (M-C) simulation in discretized collective variable space (speciﬁcally, on the same grid used by ABF to discretize the free energy gradient). By default, a history-dependent bias (similar in spirit to metadynamics) is used: at each M-C step, the bias at the current position is incremented by a preset amount (the hill height). Upon convergence, this bias counteracts optimally the underlying gradient; it is negated to obtain the estimate of the free energy surface.

abf_integrate is invoked using the command-line:

abf_integrate

The gradient ﬁle name is provided ﬁrst, followed by other parameters in any order. They are described below, with their default value in square brackets:

- -n: number of M-C steps to be performed; by default, a minimal number of steps is chosen based on the size of the grid, and the integration runs until a convergence criterion is satisﬁed (based on the RMSD between the target gradient and the real PMF gradient)
- -t: temperature for M-C sampling (unrelated to the simulation temperature) [500 K]
- -m: use metadynamics-like biased sampling? (0 = false) [1]
- -h: increment for the history-dependent bias (“hill height”) [0.01 kcal/mol]
- -f: if non-zero, this factor is used to scale the increment stepwise in the second half of the M-C sampling to reﬁne the free energy estimate [0.5]

Using the default values of all parameters should give reasonable results in most cases.

abf_integrate produces the following output ﬁles:

_file>.pmf: computed free energy surface _file>.histo: histogram of M-C sampling (not usable in a straightforward way if the history-dependent bias has been applied) _file>.est: estimated gradient of the calculated free energy surface (from ﬁnite diﬀerences) _file>.dev: deviation between the user-provided numerical gradient and the actual gradient of the calculated free energy surface. The RMS norm of this vector ﬁeld is used as a convergence criteria and displayed periodically during the integration.

Note: Typically, the “deviation” vector ﬁeld does not vanish as the integration converges. This happens because the numerical estimate of the gradient does not exactly derive from a potential, due to numerical approximations used to obtain it (ﬁnite sampling and discretization on a grid).

Extended-system ABF (eABF) is a variant of ABF (7.1) where the bias is not applied directly to the collective variable, but to an extended coordinate (“ﬁctitious variable”) λ that evolves dynamically according to Newtonian or Langevin dynamics. Such an extended coordinate is enabled for a given colvar using the extendedLagrangian and associated keywords (4.3). The theory of eABF and the present implementation are documented in detail in reference [15].

Deﬁning an ABF bias on a colvar wherein the extendedLagrangian option is active will perform eABF; there is no dedicated option.

The extended variable λ is coupled to the colvar z = ξ(q) by the harmonic potential (k∕2)(z−λ)^{2}. Under eABF
dynamics, the adaptive bias on λ is the running estimate of the average spring force:

| (21) |

where the angle brackets indicate a canonical average conditioned by λ = λ^{∗}. At long simulation
times, eABF produces a ﬂat histogram of the extended variable λ, and a ﬂattened histogram of ξ ,
whose exact shape depends on the strength of the coupling as deﬁned by extendedFluctuation in the
colvar. Coupling should be somewhat loose for faster exploration and convergence, but strong enough
that the bias does help overcome barriers along the colvar ξ .[15] Distribution of the colvar may be
assessed by plotting its histogram, which is written to the outputName.zcount ﬁle in every eABF
simulation. Note that a histogram bias (7.9) applied to an extended-Lagrangian colvar will access the
extended degree of freedom λ, not the original colvar ξ ; however, the joint histogram may be explicitly
requested by listing the name of the colvar twice in a row within the colvars parameter of the histogram
block.

The eABF PMF is that of the coordinate λ, it is not exactly the free energy proﬁle of ξ . That quantity can be calculated based on the CZAR estimator.

The corrected z-averaged restraint (CZAR) estimator is described in detail in reference [15]. It is computed automatically in eABF simulations, regardless of the number of colvars involved. Note that ABF may also be applied on a combination of extended and non-extended colvars; in that case, CZAR still provides an unbiased estimate of the free energy gradient.

CZAR estimates the free energy gradient as:

| (22) |

where z = ξ(q) is the colvar, λ is the extended variable harmonically coupled to z with a force constant k, and (z) is the observed distribution (histogram) of z, aﬀected by the eABF bias.

Parameters for the CZAR estimator are:

- CZARestimator ⟨Calculate CZAR estimator of the free energy?⟩

Context: abf

Acceptable values: boolean

Default value: yes

Description: This option is only available when ABF is performed on extended-Lagrangian colvars. When enabled, it triggers calculation of the free energy following the CZAR estimator. - writeCZARwindowFile ⟨Write internal data from CZAR to a separate ﬁle?⟩

Context: abf

Acceptable values: boolean

Default value: no

Description: When this option is enabled, eABF simulations will write a ﬁle containing the z-averaged restraint force under the name outputName.zgrad. The same information is always included in the colvars state ﬁle, which is suﬃcient for restarting an eABF simulation. These separate ﬁle is only useful when joining adjacent windows from a stratiﬁed eABF simulation, either to continue the simulation in a broader window or to compute a CZAR estimate of the PMF over the full range of the coordinate(s).

Similar to ABF, the CZAR estimator produces two output ﬁles in multicolumn text format:

- outputName.czar.grad: current estimate of the free energy gradient (grid), in multicolumn;
- outputName.czar.pmf: only for one-dimensional calculations, integrated free energy proﬁle or PMF.

The sampling histogram associated with the CZAR estimator is the z-histogram, which is written in the ﬁle outputName.zcount.

The metadynamics method uses a history-dependent potential [16] that generalizes to any type of colvars the
conformational ﬂooding [17] and local elevation [18] methods, originally formulated to use as colvars the principal
components of a covariance matrix or a set of dihedral angles, respectively. The metadynamics potential on the
colvars ξ = (ξ_{1},ξ_{2},…,ξ_{Ncv}) is deﬁned as:

| (23) |

where V_{meta} is the history-dependent potential acting on the current values of the colvars ξ , and depends only
parametrically on the previous values of the colvars. V_{meta} is constructed as a sum of N_{cv}-dimensional repulsive
Gaussian “hills”, whose height is a chosen energy constant W , and whose centers are the previously explored
conﬁgurations .

During the simulation, the system evolves towards the nearest minimum of the “eﬀective” potential of mean
force Ã(ξ), which is the sum of the “real” underlying potential of mean force A(ξ) and the the metadynamics
potential, V_{meta}(ξ). Therefore, at any given time the probability of observing the conﬁguration ξ^{∗} is
proportional to exp: this is also the probability that a new Gaussian “hill” is added at that
conﬁguration. If the simulation is run for a suﬃciently long time, each local minimum is canceled out by the
sum of the Gaussian “hills”. At that stage the “eﬀective” potential of mean force Ã(ξ) is constant, and
−V_{meta}(ξ) is an accurate estimator of the “real” potential of mean force A(ξ), save for an additive
constant:

| (24) |

Assuming that the set of collective variables includes all relevant degrees of freedom, the predicted error of the
estimate is a simple function of the correlation times of the colvars τ_{ξi}, and of the user-deﬁned parameters W , σ_{ξi}
and δt [19]. In typical applications, a good rule of thumb can be to choose the ratio W∕δt much smaller than
κ_{B}T ∕τ_{ξ}, where τ_{ξ} is the longest among ξ ’s correlation times: σ_{ξi} then dictates the resolution of the calculated
PMF.

To enable a metadynamics calculation, a metadynamics block must be deﬁned in the Colvars conﬁguration ﬁle.
Its mandatory keywords are colvars, which lists all the variables involved, and hillWeight, which speciﬁes the
weight parameter W . The parameters δt and σ_{ξ} speciﬁed by the optional keywords newHillFrequency and
hillWidth:

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- outputEnergy: see deﬁnition of outputEnergy in sec. 7 (biasing and analysis methods)
- hillWeight ⟨Height of each hill (kcal/mol)⟩

Context: metadynamics

Acceptable values: positive decimal

Description: This option sets the height W of the Gaussian hills that are added during this run. Lower values provide more accurate sampling of the system’s degrees of freedom at the price of longer simulation times to complete a PMF calculation based on metadynamics. - newHillFrequency ⟨Frequency of hill creation⟩

Context: metadynamics

Acceptable values: positive integer

Default value: 1000

Description: This option sets the number of integration steps after which a new hill is added to the metadynamics potential. Its value determines the parameter δt in eq. 23. Higher values provide more accurate sampling at the price of longer simulation times to complete a PMF calculation. - hillWidth ⟨Relative width of a Gaussian hill with respect to the colvar’s width⟩

Context: metadynamics

Acceptable values: positive decimal

Default value: ∕2

Description: The Gaussian width along each colvar, 2σ_{ξi}, is set as the product between this number and the colvar’s parameter w_{i}given by width (see 4.1); such product is printed in the standard output of VMD. The default value of this number gives a Gaussian hill function whose volume is equal to the product of ∏_{i}w_{i}, the volume of one histogram bin (see 7.9), and W . Tip: use this property to estimate the fraction of colvar space covered by the Gaussian bias within a given simulation time. When useGrids is on, the default value also gives acceptable discretization errors [1]: for smoother visualization, this parameter may be increased and the width w_{i}decreased in the same proportion. Note: values smaller than 1 are not recommended.

When interpolating grids are enabled (default behavior), the PMF is written every colvarsRestartFrequency steps to the ﬁle outputName.pmf. The following two options allow to control this behavior and to visually track statistical convergence:

- writeFreeEnergyFile ⟨Periodically write the PMF for visualization⟩

Context: metadynamics

Acceptable values: boolean

Default value: on

Description: When useGrids and this option are on, the PMF is written every colvarsRestartFrequency steps. - keepFreeEnergyFiles ⟨Keep all the PMF ﬁles⟩

Context: metadynamics

Acceptable values: boolean

Default value: off

Description: When writeFreeEnergyFile and this option are on, the step number is included in the ﬁle name, thus generating a series of PMF ﬁles. Activating this option can be useful to follow more closely the convergence of the simulation, by comparing PMFs separated by short times.

Note: when Gaussian hills are deposited near lowerBoundary or upperBoundary (see 4.1) and interpolating grids are used (default behavior), their truncation can give rise to accumulating errors. In these cases, as a measure of fault-tolerance all Gaussian hills near the boundaries are included in the output state ﬁle, and are recalculated analytically whenever the colvar falls outside the grid’s boundaries. (Such measure protects the accuracy of the calculation, and can only be disabled by hardLowerBoundary or hardUpperBoundary.) To avoid gradual loss of performance and growth of the state ﬁle, either one of the following solutions is recommended:

- enabling the option expandBoundaries, so that the grid’s boundaries are automatically recalculated whenever necessary; the resulting .pmf will have its abscissas expanded accordingly;
- applying a harmonicWalls bias with the wall locations well within the interval delimited by lowerBoundary and upperBoundary.

The following options control the computational cost of metadynamics calculations, but do not aﬀect results. Default values are chosen to minimize such cost with no loss of accuracy.

- useGrids ⟨Interpolate the hills with grids⟩

Context: metadynamics

Acceptable values: boolean

Default value: on

Description: This option discretizes all hills for improved performance, accumulating their energy and their gradients on two separate grids of equal spacing. Grids are deﬁned by the values of lowerBoundary, upperBoundary and width for each colvar. Currently, this option is implemented for all types of variables except the non-scalar types (distanceDir or orientation). If expandBoundaries is deﬁned in one of the colvars, grids are automatically expanded along the direction of that colvar. - rebinGrids ⟨Recompute the grids when reading a state ﬁle⟩

Context: metadynamics

Acceptable values: boolean

Default value: off

Description: When restarting from a state ﬁle, the grid’s parameters (boundaries and widths) saved in the state ﬁle override those in the conﬁguration ﬁle. Enabling this option forces the grids to match those in the current conﬁguration ﬁle.

The following options deﬁne the conﬁguration for the “well-tempered” metadynamics approach [20]:

- wellTempered ⟨Perform well-tempered metadynamics⟩

Context: metadynamics

Acceptable values: boolean

Default value: off

Description: If enabled, this ﬂag causes well-tempered metadynamics as described by Barducci et al.[20] to be performed, rather than standard metadynamics. The parameter biasTemperature is then required.This feature was contributed by Li Li (Luthey-Schulten group, Departement of Chemistry, UIUC). - biasTemperature ⟨Temperature bias for well-tempered metadynamics⟩

Context: metadynamics

Acceptable values: positive decimal

Description: When running metadynamics in the long time limit, collective variable space is sampled to a modiﬁed temperature T +ΔT . In conventional metadynamics, the temperature “boost” ΔT would constantly increases with time. Instead, in well-tempered metadynamics ΔT must be deﬁned by the user via biasTemperature. The written PMF includes the scaling factor (T +ΔT )∕ΔT [20]. A careful choice of ΔT determines the sampling and convergence rate, and is hence crucial to the success of a well-tempered metadynamics simulation.

The following options deﬁne metadynamics calculations with more than one replica:

- multipleReplicas ⟨Multiple replicas metadynamics⟩

Context: metadynamics

Acceptable values: boolean

Default value: off

Description: If this option is on, multiple (independent) replica of the same system can be run at the same time, and their hills will be combined to obtain a single PMF [21]. Replicas are identiﬁed by the value of replicaID. Communication is done by ﬁles: each replica must be able to read the ﬁles created by the others, whose paths are communicated through the ﬁle replicasRegistry. This ﬁle, and the ﬁles listed in it, are read every replicaUpdateFrequency steps. Every time the colvars state ﬁle is written (colvarsRestartFrequency), the ﬁle:

“outputName.colvars.name.replicaID.state” is also written, containing the state of the metadynamics bias for replicaID. In the time steps between colvarsRestartFrequency, new hills are temporarily written to the ﬁle:

“outputName.colvars.name.replicaID.hills”, which serves as communication buﬀer. These ﬁles are only required for communication, and may be deleted after a new MD run is started with a diﬀerent outputName. - replicaID ⟨Set the identiﬁer for this replica⟩

Context: metadynamics

Acceptable values: string

Description: If multipleReplicas is on, this option sets a unique identiﬁer for this replica. All replicas should use identical collective variable conﬁgurations, except for the value of this option. - replicasRegistry ⟨Multiple replicas database ﬁle⟩

Context: metadynamics

Acceptable values: UNIX ﬁlename

Default value: “name.replica_files.txt”

Description: If multipleReplicas is on, this option sets the path to the replicas’ database ﬁle. - replicaUpdateFrequency ⟨How often hills are communicated between replicas⟩

Context: metadynamics

Acceptable values: positive integer

Default value: newHillFrequency

Description: If multipleReplicas is on, this option sets the number of steps after which each replica (re)reads the other replicas’ ﬁles. The lowest meaningful value of this number is newHillFrequency. If access to the ﬁle system is signiﬁcantly aﬀecting the simulation performance, this number can be increased, at the price of reduced synchronization between replicas. Values higher than colvarsRestartFrequency may not improve performance signiﬁcantly. - dumpPartialFreeEnergyFile ⟨Periodically write the contribution to the PMF from this replica⟩

Context: metadynamics

Acceptable values: boolean

Default value: on

Description: When multipleReplicas is on, the ﬁle outputName.pmf contains the combined PMF from all replicas, provided that useGrids is on (default). Enabling this option produces an additional ﬁle outputName.partial.pmf, which can be useful to quickly monitor the contribution of each replica to the PMF.

The following options may be useful only for applications that go beyond the calculation of a PMF by metadynamics:

- name ⟨Name of this metadynamics instance⟩

Context: metadynamics

Acceptable values: string

Default value: “meta” + rank number

Description: This option sets the name for this metadynamics instance. While it is not advisable to use more than one metadynamics instance within the same simulation, this allows to distinguish each instance from the others. If there is more than one metadynamics instance, the name of this bias is included in the metadynamics output ﬁle names, such as e.g. the .pmf ﬁle. - keepHills ⟨Write each individual hill to the state ﬁle⟩

Context: metadynamics

Acceptable values: boolean

Default value: off

Description: When useGrids and this option are on, all hills are saved to the state ﬁle in their analytic form, alongside their grids. This makes it possible to later use exact analytic Gaussians for rebinGrids. To only keep track of the history of the added hills, writeHillsTrajectory is preferable. - writeHillsTrajectory ⟨Write a log of new hills⟩

Context: metadynamics

Acceptable values: boolean

Default value: off

Description: If this option is on, a logﬁle is written by the metadynamics bias, with the name “outputName.colvars.<name>.hills.traj”, which can be useful to follow the time series of the hills. When multipleReplicas is on, its name changes to

“outputName.colvars.<name>.<replicaID>.hills.traj”. This ﬁle can be used to quickly visualize the positions of all added hills, in case newHillFrequency does not coincide with colvarsRestartFrequency.

The harmonic biasing method may be used to enforce ﬁxed or moving restraints, including variants of Steered and Targeted MD. Within energy minimization runs, it allows for restrained minimization, e.g. to calculate relaxed potential energy surfaces. In the context of the Colvars module, harmonic potentials are meant according to their textbook deﬁnition:

| (25) |

Note that this diﬀers from harmonic bond and angle potentials in common force ﬁelds, where the factor of one half is typically omitted, resulting in a non-standard deﬁnition of the force constant.

The formula above includes the characteristic length scale w_{ξ} of the colvar ξ (keyword width, see 4.1) to allow
the deﬁnition of a multi-dimensional restraint with a uniﬁed force constant:

| (26) |

If one-dimensional or homogeneous multi-dimensional restraints are deﬁned, and there are no other uses for the
parameter w_{ξ}, the parameter width can be left at its default value of 1.

A harmonic restraint is set up by a harmonic {...} block, which may contain (in addition to the standard option colvars) the following keywords:

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- outputEnergy: see deﬁnition of outputEnergy in sec. 7 (biasing and analysis methods)
- forceConstant ⟨Scaled force constant (kcal/mol)⟩

Context: harmonic

Acceptable values: positive decimal

Default value: 1.0

Description: This deﬁnes a scaled force constant k for the harmonic potential (eq. 26). To ensure consistency for multidimensional restraints, it is divided internally by the square of the speciﬁc width for each colvar involved (which is 1 by default), so that all colvars are eﬀectively dimensionless and of commensurate size. For instance, setting a scaled force constant of 10 kcal/mol acting on two colvars, an angle with a width of 5 degrees and a distance with a width of 0.5 Å, will apply actual force constants of 0.4 kcal/mol×degree^{−2}for the angle and 40 kcal/mol/Å^{2}for the distance. - centers ⟨Initial harmonic restraint centers⟩

Context: harmonic

Acceptable values: space-separated list of colvar values

Description: The centers (equilibrium values) of the restraint, ξ_{0}, are entered here. The number of values must be the number of requested colvars. Each value is a decimal number if the corresponding colvar returns a scalar, a “(x, y, z)” triplet if it returns a unit vector or a vector, and a “(q0, q1, q2, q3)” quadruplet if it returns a rotational quaternion. If a colvar has periodicities or symmetries, its closest image to the restraint center is considered when calculating the harmonic potential.

Tip: A complex set of restraints can be applied to a system, by deﬁning several colvars, and applying one or more harmonic restraints to diﬀerent groups of colvars. In some cases, dozens of colvars can be deﬁned, but their value may not be relevant: to limit the size of the colvars trajectory ﬁle, it may be wise to disable outputValue for such “ancillary” variables, and leave it enabled only for “relevant” ones.

The following options allow to change gradually the centers of the harmonic restraints during a simulations. When the centers are changed continuously, a steered MD in a collective variable space is carried out.

- targetCenters ⟨Steer the restraint centers towards these targets⟩

Context: harmonic

Acceptable values: space-separated list of colvar values

Description: When deﬁned, the current centers will be moved towards these values during the simulation. By default, the centers are moved over a total of targetNumSteps steps by a linear interpolation, in the spirit of Steered MD. If targetNumStages is set to a nonzero value, the change is performed in discrete stages, lasting targetNumSteps steps each. This second mode may be used to sample successive windows in the context of an Umbrella Sampling simulation. When continuing a simulation run, the centers speciﬁed in the conﬁguration ﬁle <colvarsConfig> are overridden by those saved in the restart ﬁle <colvarsInput>. To perform Steered MD in an arbitrary space of colvars, it is suﬃcient to use this option and enable outputAccumulatedWork and/or outputAppliedForce within each of the colvars involved. - targetNumSteps ⟨Number of steps for steering⟩

Context: harmonic

Acceptable values: positive integer

Description: In single-stage (continuous) transformations, deﬁnes the number of MD steps required to move the restraint centers (or force constant) towards the values speciﬁed with targetCenters or targetForceConstant. After the target values have been reached, the centers (resp. force constant) are kept ﬁxed. In multi-stage transformations, this sets the number of MD steps per stage. - outputCenters ⟨Write the current centers to the trajectory ﬁle⟩

Context: harmonic

Acceptable values: boolean

Default value: off

Description: If this option is chosen and colvarsTrajFrequency is not zero, the positions of the restraint centers will be written to the trajectory ﬁle during the simulation. This option allows to conveniently extract the PMF from the colvars trajectory ﬁles in a steered MD calculation.

Note on restarting moving restraint simulations: Information about the current step and stage of a simulation with moving restraints is stored in the restart ﬁle (state ﬁle). Thus, such simulations can be run in several chunks, and restarted directly using the same colvars conﬁguration ﬁle. In case of a restart, the values of parameters such as targetCenters, targetNumSteps, etc. should not be changed manually.

The centers of the harmonic restraints can also be changed in discrete stages: in this cases a one-dimensional umbrella sampling simulation is performed. The sampling windows in simulation are calculated in sequence. The colvars trajectory ﬁle may then be used both to evaluate the correlation times between consecutive windows, and to calculate the frequency distribution of the colvar of interest in each window. Furthermore, frequency distributions on a predeﬁned grid can be automatically obtained by using the histogram bias (see 7.9).

To activate an umbrella sampling simulation, the same keywords as in the previous section can be used, with the addition of the following:

- targetNumStages ⟨Number of stages for steering⟩

Context: harmonic

Acceptable values: non-negative integer

Default value: 0

Description: If non-zero, sets the number of stages in which the restraint centers or force constant are changed to their target values. If zero, the change is continuous. Each stage lasts targetNumSteps MD steps. To sample both ends of the transformation, the simulation should be run for targetNumSteps × (targetNumStages + 1).

The force constant of the harmonic restraint may also be changed to equilibrate [22].

- targetForceConstant ⟨Change the force constant towards this value⟩

Context: harmonic

Acceptable values: positive decimal

Description: When deﬁned, the current forceConstant will be moved towards this value during the simulation. Time evolution of the force constant is dictated by the targetForceExponent parameter (see below). By default, the force constant is changed smoothly over a total of targetNumSteps steps. This is useful to introduce or remove restraints in a progressive manner. If targetNumStages is set to a nonzero value, the change is performed in discrete stages, lasting targetNumSteps steps each. This second mode may be used to compute the conformational free energy change associated with the restraint, within the FEP or TI formalisms. For convenience, the code provides an estimate of the free energy derivative for use in TI. A more complete free energy calculation (particularly with regard to convergence analysis), while not handled by the Colvars module, can be performed by post-processing the colvars trajectory, if colvarsTrajFrequency is set to a suitably small value. It should be noted, however, that restraint free energy calculations may be handled more eﬃciently by an indirect route, through the determination of a PMF for the restrained coordinate.[22] - targetForceExponent ⟨Exponent in the time-dependence of the force constant⟩

Context: harmonic

Acceptable values: decimal equal to or greater than 1.0

Default value: 1.0

Description: Sets the exponent, α, in the function used to vary the force constant as a function of time. The force is varied according to a coupling parameter λ, raised to the power α: k_{λ}= k_{0}+λ^{α}(k_{1}−k_{0}), where k_{0}, k_{λ}, and k_{1}are the initial, current, and ﬁnal values of the force constant. The parameter λ evolves linearly from 0 to 1, either smoothly, or in targetNumStages equally spaced discrete stages, or according to an arbitrary schedule set with lambdaSchedule. When the initial value of the force constant is zero, an exponent greater than 1.0 distributes the eﬀects of introducing the restraint more smoothly over time than a linear dependence, and ensures that there is no singularity in the derivative of the restraint free energy with respect to lambda. A value of 4 has been found to give good results in some tests. - targetEquilSteps ⟨Number of steps discarded from TI estimate⟩

Context: harmonic

Acceptable values: positive integer

Description: Deﬁnes the number of steps within each stage that are considered equilibration and discarded from the restraint free energy derivative estimate reported reported in the output. - lambdaSchedule ⟨Schedule of lambda-points for changing force constant⟩

Context: harmonic

Acceptable values: list of real numbers between 0 and 1

Description: If speciﬁed together with targetForceConstant, sets the sequence of discrete λ values that will be used for diﬀerent stages.

If the restraint centers or force constant are changed continuosly (targetNumStages undeﬁned) it is possible to record the net work performed by the changing restraint:

- outputAccumulatedWork ⟨Write the accumulated work of the changing restraint to the Colvars
trajectory ﬁle⟩

Context: harmonic

Acceptable values: boolean

Default value: off

Description: If targetCenters or targetForceConstant are deﬁned and this option is enabled, the accumulated work from the beginning of the simulation will be written to the trajectory ﬁle (colvarsTrajFrequency must be non-zero). When the simulation is continued from a state ﬁle, the previously accumulated work is included in the integral. This option allows to conveniently extract the estimated PMF of a steered MD calculation (when targetCenters is used), or of other simulation protocols.

The harmonicWalls {...} bias is closely related to the harmonic bias (see 7.4), with the following two diﬀerences: (i) instead of a center a lower wall and/or an upper wall are deﬁned, outside of which the bias implements a half-harmonic potential;

| (27) |

where ξ_{lower} and ξ_{upper} are the lower and upper wall thresholds, respectively; (ii) because an interval between two
walls is deﬁned, only scalar variables can be used (but any number of variables can be deﬁned, and the wall bias is
intrinsically multi-dimensional).

Note: this bias replaces the keywords lowerWall, lowerWallConstant, upperWall and upperWallConstant deﬁned in the colvar context (see 4). These keywords are still supported, but are deprecated for future uses.

The harmonicWalls bias implements the following options:

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- outputEnergy: see deﬁnition of outputEnergy in sec. 7 (biasing and analysis methods)
- lowerWalls ⟨Position of the lower wall⟩

Context: colvar

Acceptable values: Space-separated list of decimals

Description: Deﬁnes the values ξ_{lower}below which a conﬁning restraint on the colvar is applied to each colvar ξ . - upperWalls ⟨Position of the lower wall⟩

Context: colvar

Acceptable values: Space-separated list of decimals

Description: Deﬁnes the values ξ_{upper}above which a conﬁning restraint on the colvar is applied to each colvar ξ . - forceConstant: see deﬁnition of forceConstant in sec. 7.4 (Harmonic restraints)
- lowerWallConstant ⟨Force constant for the lower wall⟩

Context: harmonicWalls

Acceptable values: positive decimal

Default value: forceConstant

Description: When both sets of walls are deﬁned (lower and upper), this keyword allows setting diﬀerent force constants for them. The force constant reported in the output as “k”, and used in the change of force constant scheme, is the geometric mean of the two. - upperWallConstant: analogous to lowerWallConstant
- targetForceConstant: see deﬁnition of targetForceConstant in sec. 7.4 (Harmonic restraints)
- targetForceConstant ⟨Change the force constant(s) towards this value⟩

Context: harmonicWalls

Acceptable values: positive decimal

Description: This keyword allows changing either one or both of the wall force constants over time. In the case that lowerWallConstant and upperWallConstant have the same value, the behavior of this keyword is identical to the corresponding keyword in the harmonic restraint; otherwise, the change schedule is applied to the geometric mean of the two constant. When only one set of walls is deﬁned (lowerWall or upperWalls), only the respective force constant is changed. Note: if only one of the two force constants is meant to change over time, it is possible to use two instances of harmonicWalls, and apply the changing schedule only to one of them. - targetNumSteps: see deﬁnition of targetNumSteps in sec. 7.4 (Harmonic restraints)
- targetForceExponent: see deﬁnition of targetForceExponent in sec. 7.4 (Harmonic restraints)
- targetEquilSteps: see deﬁnition of targetEquilSteps in sec. 7.4 (Harmonic restraints)
- targetNumStages: see deﬁnition of targetNumStages in sec. 7.4 (Harmonic restraints)
- lambdaSchedule: see deﬁnition of lambdaSchedule in sec. 7.4 (Harmonic restraints)
- outputAccumulatedWork: see deﬁnition of outputAccumulatedWork in sec. 7.4 (Harmonic restraints)

The linear restraint biasing method is used to minimally bias a simulation. There is generally a unique strength of bias for each CV center, which means you must know the bias force constant speciﬁcally for the center of the CV. This force constant may be found by using experiment directed simulation described in section 7.8. Please cite Pitera and Chodera when using [23].

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- forceConstant ⟨Scaled force constant (kcal/mol)⟩

Context: linear

Acceptable values: positive decimal

Default value: 1.0

Description: This deﬁnes a scaled force constant for the linear bias. To ensure consistency for multidimensional restraints, it is divided internally by the speciﬁc width for each colvar involved (which is 1 by default), so that all colvars are eﬀectively dimensionless and of commensurate size. - centers ⟨Initial linear restraint centers⟩

Context: linear

Acceptable values: space-separated list of colvar values

Description: These are analogous to the centers keyword of the harmonic restraint. Although they do not aﬀect dynamics, they are here necessary to ensure a well-deﬁned energy for the linear bias. - targetForceConstant: see deﬁnition of targetForceConstant in sec. 7.4 (Harmonic restraints)
- targetNumSteps: see deﬁnition of targetNumSteps in sec. 7.4 (Harmonic restraints)
- targetForceExponent: see deﬁnition of targetForceExponent in sec. 7.4 (Harmonic restraints)
- targetEquilSteps: see deﬁnition of targetEquilSteps in sec. 7.4 (Harmonic restraints)
- targetNumStages: see deﬁnition of targetNumStages in sec. 7.4 (Harmonic restraints)
- lambdaSchedule: see deﬁnition of lambdaSchedule in sec. 7.4 (Harmonic restraints)
- outputAccumulatedWork: see deﬁnition of outputAccumulatedWork in sec. 7.4 (Harmonic restraints)

Experiment directed simulation applies a linear bias with a changing force constant. Please cite White and Voth [24] when using this feature. As opposed to that reference, the force constant here is scaled by the width corresponding to the biased colvar. In White and Voth, each force constant is scaled by the colvars set center. The bias converges to a linear bias, after which it will be the minimal possible bias. You may also stop the simulation, take the median of the force constants (ForceConst) found in the colvars trajectory ﬁle, and then apply a linear bias with that constant. All the notes about units described in sections 7.7 and 7.4 apply here as well. This is not a valid simulation of any particular statistical ensemble and is only an optimization algorithm until the bias has converged.

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- centers ⟨Collective variable centers⟩

Context: alb

Acceptable values: space-separated list of colvar values

Description: The desired center (equilibrium values) which will be sought during the adaptive linear biasing. The number of values must be the number of requested colvars. Each value is a decimal number if the corresponding colvar returns a scalar, a “(x, y, z)” triplet if it returns a unit vector or a vector, and a “q0, q1, q2, q3)” quadruplet if it returns a rotational quaternion. If a colvar has periodicities or symmetries, its closest image to the restraint center is considered when calculating the linear potential. - updateFrequency ⟨The duration of updates⟩

Context: alb

Acceptable values: An integer

Description: This is, N, the number of simulation steps to use for each update to the bias. This determines how long the system requires to equilibrate after a change in force constant (N∕2), how long statistics are collected for an iteration (N∕2), and how quickly energy is added to the system (at most, A∕2N, where A is the forceRange). Until the force constant has converged, the method as described is an optimization procedure and not an integration of a particular statistical ensemble. It is important that each step should be uncorrelated from the last so that iterations are independent. Therefore, N should be at least twice the autocorrelation time of the collective variable. The system should also be able to dissipate energy as fast as N∕2, which can be done by adjusting thermostat parameters. Practically, N has been tested successfully at signiﬁcantly shorter than the autocorrelation time of the collective variables being biased and still converge correctly. - forceRange ⟨The expected range of the force constant in units of energy⟩

Context: alb

Acceptable values: A space-separated list of decimal numbers

Default value: 3 k_{b}T

Description: This is largest magnitude of the force constant which one expects. If this parameter is too low, the simulation will not converge. If it is too high the simulation will waste time exploring values that are too large. A value of 3 k_{b}T has worked well in the systems presented as a ﬁrst choice. This parameter is dynamically adjusted over the course of a simulation. The beneﬁt is that a bad guess for the forceRange can be corrected. However, this can lead to large amounts of energy being added over time to the system. To prevent this dynamic update, add hardForceRange yes as a parameter - rateMax ⟨The maximum rate of change of force constant⟩

Context: alb

Acceptable values: A list of space-separated real numbers

Description: This optional parameter controls how much energy is added to the system from this bias. Tuning this separately from the updateFrequency and forceRange can allow for large bias changes but with a low rateMax prevents large energy changes that can lead to instability in the simulation.

The histogram feature is used to record the distribution of a set of collective variables in the form of a N-dimensional histogram.

As with any other biasing and analysis method, when a histogram is applied to an extended-system colvar (4.3), it accesses the value of the ﬁctitious coordinate rather than that of the “true” colvar. A joint histogram of the “true” colvar and the ﬁctitious coordinate may be obtained by specifying the colvar name twice in a row in the colvars parameter: the ﬁrst instance will be understood as the “true” colvar, and the second, as the ﬁctitious coordinate.

A histogram block may deﬁne the following parameters:

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- outputFreq ⟨Frequency (in timesteps) at which the histogram ﬁles are refreshed⟩

Context: histogram

Acceptable values: positive integer

Default value: colvarsRestartFrequency

Description: The histogram data are written to ﬁles at the given time interval. A value of 0 disables the creation of these ﬁles (note: all data to continue a simulation are still included in the state ﬁle). - outputFile ⟨Write the histogram to a ﬁle⟩

Context: histogram

Acceptable values: UNIX ﬁlename

Default value: outputName.<name>.dat

Description: Name of the ﬁle containing histogram data (multicolumn format), which is written every outputFreq steps. For the special case of 2 variables, Gnuplot may be used to visualize this ﬁle. - outputFileDX ⟨Write the histogram to a ﬁle⟩

Context: histogram

Acceptable values: UNIX ﬁlename

Default value: outputName.<name>.dat

Description: Name of the ﬁle containing histogram data (OpenDX format), which is written every outputFreq steps. For the special case of 3 variables, VMD may be used to visualize this ﬁle. - gatherVectorColvars ⟨Treat vector variables as multiple observations of a scalar variable?⟩

Context: histogram

Acceptable values: UNIX ﬁlename

Default value: off

Description: When this is set to on, the components of a multi-dimensional colvar (e.g. one based on cartesian, distancePairs, or a vector of scalar numbers given by scriptedFunction) are treated as multiple observations of a scalar variable. This results in the histogram being accumulated multiple times for each simulation step or iteration of cv update). When multiple vector variables are included in histogram, these must have the same length because their components are accumulated together. For example, if ξ , λ and τ are three variables of dimensions 5, 5 and 1, respectively, for each iteration 5 triplets (ξ_{i},λ_{i},τ) (i = 1,…5) are accumulated into a 3-dimensional histogram. - weights ⟨Treat vector variables as multiple observations of a scalar variable?⟩

Context: histogram

Acceptable values: list of space-separated decimals

Default value: all weights equal to 1

Description: When gatherVectorColvars is on, the components of each multi-dimensional colvar are accumulated with a diﬀerent weight. For example, if x and y are two distinct cartesian variables deﬁned on the same group of atoms, the corresponding 2D histogram can be weighted on a per-atom basis: to compute an electron density map, it is possible to use weights [$sel get atomicnumber] in the deﬁnition of histogram.

Like the ABF and metadynamics biases, histogram uses the parameters lowerBoundary, upperBoundary, and width to deﬁne its grid. These values can be overridden if a conﬁguration block histogramGrid { …} is provided inside the conﬁguration of histogram. The options supported inside this conﬁguration block are:

- lowerBoundaries ⟨Lower boundaries of the grid⟩

Context: histogramGrid

Acceptable values: list of space-separated decimals

Description: This option deﬁnes the lower boundaries of the grid, overriding any values deﬁned by the lowerBoundary keyword of each colvar. Note that when gatherVectorColvars is on, each vector variable is automatically treated as a scalar, and a single value should be provided for it. - upperBoundaries: analogous to lowerBoundaries
- widths: analogous to lowerBoundaries

The histogramRestraint bias implements a continuous potential of many variables (or of a single
high-dimensional variable) aimed at reproducing a one-dimensional statistical distribution that is provided by the
user. The M variables (ξ_{1},…,ξ_{M}) are interpreted as multiple observations of a random variable ξ with unknown
probability distribution. The potential is minimized when the histogram h(ξ), estimated as a sum of Gaussian
functions centered at (ξ_{1},…,ξ_{M}), is equal to the reference histogram h_{0}(ξ):

| (28) |

| (29) |

When used in combination with a distancePairs multi-dimensional variable, this bias implements the reﬁnement algorithm against ESR/DEER experiments published by Shen et al [25].

This bias behaves similarly to the histogram bias with the gatherVectorColvars option, with the important diﬀerence that all variables are gathered, resulting in a one-dimensional histogram. Future versions will include support for multi-dimensional histograms.

The list of options is as follows:

- name: see deﬁnition of name in sec. 7 (biasing and analysis methods)
- colvars: see deﬁnition of colvars in sec. 7 (biasing and analysis methods)
- outputEnergy: see deﬁnition of outputEnergy in sec. 7 (biasing and analysis methods)
- lowerBoundary ⟨Lower boundary of the colvar grid⟩

Context: histogramRestraint

Acceptable values: decimal

Description: Deﬁnes the lowest end of the interval where the reference distribution h_{0}(ξ) is deﬁned. Exactly one value must be provided, because only one-dimensional histograms are supported by the current version. - upperBoundary: analogous to lowerBoundary
- width ⟨Width of the colvar grid⟩

Context: histogramRestraint

Acceptable values: positive decimal

Description: Deﬁnes the spacing of the grid where the reference distribution h_{0}(ξ) is deﬁned. - gaussianSigma ⟨Standard deviation of the approximating Gaussian⟩

Context: histogramRestraint

Acceptable values: positive decimal

Default value: 2 ×width

Description: Deﬁnes the parameter σ in eq. 29. - forceConstant ⟨Force constant (kcal/mol)⟩

Context: histogramRestraint

Acceptable values: positive decimal

Default value: 1.0

Description: Deﬁnes the parameter k in eq. 28. - refHistogram ⟨Reference histogram h
_{0}(ξ)⟩

Context: histogramRestraint

Acceptable values: space-separated list of M positive decimals

Description: Provides the values of h_{0}(ξ) consecutively. The mid-point convention is used, i.e. the ﬁrst point that should be included is for ξ = lowerBoundary+width/2. If the integral of h_{0}(ξ) is not normalized to 1, h_{0}(ξ) is rescaled automatically before use. - refHistogramFile ⟨Reference histogram h
_{0}(ξ)⟩

Context: histogramRestraint

Acceptable values: UNIX ﬁle name

Description: Provides the values of h_{0}(ξ) as contents of the corresponding ﬁle (mutually exclusive with refHistogram). The format is that of a text ﬁle, with each line containing the space-separated values of ξ and h_{0}(ξ). The same numerical conventions as refHistogram are used. - writeHistogram ⟨Periodically write the instantaneous histogram h(ξ)⟩

Context: metadynamics

Acceptable values: boolean

Default value: off

Description: If on, the histogram h(ξ) is written every colvarsRestartFrequency steps to a ﬁle with the name outputName.<name>.hist.dat This is useful to diagnose the convergence of h(ξ) against h_{0}(ξ).

Rather than using the biasing methods described above, it is possible to apply biases provided at run time as a Tcl script. This option, also available in NAMD, can be useful to test a new algorithm to be used in a MD simulation.

- scriptedColvarForces ⟨Enable custom, scripted forces on colvars ⟩

Context: global

Acceptable values: boolean

Default value: off

Description: If this ﬂag is enabled, a Tcl procedure named calc_colvar_forces accepting one parameter should be deﬁned by the user. It is executed at each timestep, with the current step number as parameter, between the calculation of colvars and the application of bias forces. This procedure may use the cv command to access the values of colvars and apply forces on them, eﬀectively deﬁning custom collective variable biases.

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