colvar | A collective variable (main class); to be defined, it needs at least one object of a derived class of colvar::cvc; it calculates and returns a colvarvalue object |
alpha_angles | Colvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of phi/psi dihedral angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1]) |
angle | Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]) |
cartesian | |
coordnum | Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) |
cvc | Colvar component (base class); most implementations of cvc utilize one or more colvarmodule::atom or colvarmodule::atom_group objects to access atoms |
dihedPC | Colvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007) Based on a set of 'dihedral' cvcs |
dihedral | Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]) |
dipole_angle | Colvar component: angle between the dipole of a molecule and an axis formed by two groups of atoms(colvarvalue::type_scalar type, range [0:PI]) |
distance | Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)) |
distance_dir | Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unit3vector type, range [-1:1]x[-1:1]x[-1:1]) |
distance_inv | Colvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements(colvarvalue::type_scalar type, range (0:*)) |
distance_pairs | Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component) |
distance_vec | |
distance_xy | Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)) |
distance_z | Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*)) |
eigenvector | Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*)) |
groupcoordnum | Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) |
gyration | Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)) |
h_bond | Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1]) |
inertia | Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*)) |
inertia_z | Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*)) |
orientation | Colvar component: orientation in space of an atom group, with respect to a set of reference coordinates (colvarvalue::type_quaternion type, range [-1:1]x[-1:1]x[-1:1]x[-1:1]) |
orientation_angle | Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI)) |
orientation_proj | Colvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1]) |
rmsd | Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses colvar::orientation to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)) |
selfcoordnum | Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2]) |
spin_angle | Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI]) |
tilt | Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1]) |
colvar_grid | Grid of values of a function of several collective variables |
colvar_grid_count | Colvar_grid derived class to hold counters in discrete n-dim colvar space |
colvar_grid_gradient | Class for accumulating the gradient of a scalar function on a grid |
colvar_grid_scalar | Class for accumulating a scalar function on a grid |
colvarbias | Collective variable bias, base class |
colvarbias_abf | ABF bias |
colvarbias_alb | |
colvarbias_histogram | Histogram "bias" (does as the name says) |
colvarbias_meta | Metadynamics bias (implementation of colvarbias) |
hill | A hill for the metadynamics bias |
colvarbias_restraint | Most general definition of a colvar restraint: see derived classes for specific types (implementation of colvarbias) |
colvarbias_restraint_centers | Definition and parsing of the restraint centers |
colvarbias_restraint_centers_moving | Options to change the restraint centers over time |
colvarbias_restraint_harmonic | Harmonic bias restraint (implementation of colvarbias_restraint) |
colvarbias_restraint_harmonic_walls | Wall restraint (implementation of colvarbias_restraint) |
colvarbias_restraint_histogram | Restrain the 1D histogram of a set of variables (or of a multidimensional one) |
colvarbias_restraint_k | Definition and parsing of the force constant |
colvarbias_restraint_k_moving | Options to change the restraint force constant over time |
colvarbias_restraint_linear | Linear bias restraint (implementation of colvarbias_restraint) |
colvarbias_restraint_moving | Options to change the restraint configuration over time (shared between centers and k moving) |
colvardeps | Parent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution |
feature | |
feature_state | This contains the current state of each feature for each object |
colvarmodule | Collective variables module (main class) |
atom | Stores numeric id, mass and all mutable data for an atom, mostly used by a cvc |
atom_group | Group of atom objects, mostly used by a cvc object to gather all atomic data |
matrix2d | Arbitrary size array (two dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions) |
row | |
quaternion | 1-dimensional vector of real numbers with four components and a quaternion algebra |
rmatrix | 2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector) |
rotation | A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion) |
rvector | Vector of real numbers with three components |
vector1d | Arbitrary size array (one dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions) |
colvarparse | Base class containing parsing functions; all objects which need to parse input inherit from this |
read_block | Helper class to read a block of the type "key { ... }" from a stream and store it in a string |
colvarproxy | Interface between the collective variables module and the simulation or analysis program (NAMD, VMD, LAMMPS...). This is the base class: each interfaced program is supported by a derived class. Only pure virtual functions ("= 0") must be reimplemented to ensure baseline functionality |
colvarproxy_namd | Communication between colvars and NAMD (implementation of colvarproxy) |
colvarproxy_vmd | Communication between colvars and VMD (implementation of colvarproxy) |
colvarscript | |
colvarvalue | Value of a collective variable: this is a metatype which can be set at runtime. By default it is set to be a scalar number, and can be treated as such in all operations (this is done by most cvc implementations) |
ScriptTcl | |
SimParameters | |