A software library for molecular simulation programs, which provides a flexible and high-performance platform for present and future algorithms (reference article).
Reference manual:
- LAMMPS version: PDF HTML
- NAMD version: PDF HTML
- GROMACS version: PDF HTML
- Tinker-HP version: PDF HTML
- VMD version: PDF HTML
Example configurations:
- Check the examples repository https://github.com/Colvars/examples, and particularly the detailed instruction set.
- Check also the examples folder inside the code repository: examples include configuration files for NMR restraints, targeted MD, and to define the relative orientation of two flexible objects.
To use the latest version of this code:
- Check the LAMMPS precompiled binaries, the nightly builds of NAMD, or the alpha versions of VMD. OR
- Download this repository and run the update-colvars-code.sh script to update the source code of the program of your choice. This approach is normally useful on ly for VMD, where the source code updates are infrequent.
To report bugs or to suggest new features:
Use the Issues tab of our Github page.
To extend the code
A working implementation of a new variable or a new algorithm can be achieved already with scripted functions, without changes to the C++ code: see the reference manuals for details. Depending on how much the scripted code reuses binary code, this may be already efficient, or require changes to the underlying code.
For further flexibility and optimization, it is possible to modify the C++ code: details are available through the C++ class documentation. One notable example is adding a new type of collective variable, which is described here.
License
This software is distributed under the GNU Lesser General Public License, version 3.