Collective variables module (Colvars)

A software module for molecular simulation and analysis that provides a high-performance implementation of sampling algorithms defined on a reduced space of continuously differentiable functions (aka collective variables).

First released in 2008 as part of the standard distribution of NAMD version 2.7b1, Colvars has also been integrated in LAMMPS and VMD. In VMD, interactive use is possible both from the command line and through the Dashboard graphical user interface.

Patched releases of GROMACS that contain Colvars are also available (see below).

The functionality provided by the Colvars library includes a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.

Obtaining and using

The easiest way to obtain pre-compiled versions of Colvars is via one of following:

the molecular simulation program LAMMPS;
the molecular simulation program NAMD;
the molecular visualization program VMD.

Please check here to see which version of Colvars is included with the round-number or "stable" versions of each code.

For the molecular simulation program GROMACS, code may be compiled via our Colvars-patched releases.

Documentation

The Colvars webpage includes user documentation for the four codes, as well as a Doxygen-based developer documentation.

To reflect the different availability of features in each engine, the Colvars reference manual comes in several flavors: GROMACS LAMMPS NAMD VMD

Citing

The reference article is: G. Fiorin, M. L. Klein, and J. Hénin, Mol. Phys. 111 (22-23), 3345-3362 (2013). https://doi.org/10.1080/00268976.2013.813594 [BibTex file] [Endnote file]

Additional references for the implementation of specific features are listed in the documentation. Beginning with Colvars 2021-08-30, these references, including acknowledgments of specific code from the MD engine, are also printed to the screen/logfile when they are used.

Note to NAMD users: the NAMD reference papers (Phillips et al, 2005 and 2020) are used in some publications to acknowledge Colvars features. This is incomplete. When possible, please consider identifying and acknowledging all development efforts that supported your project. As an important clarification, most of the Colvars code was developed outside of the NAMD/VMD funding grants.

Example input

Colvars requires a configuration file, or alternatively configuration arguments given through scripting commands by the linked program.

In NAMD:

colvars on
cv configfile <Colvars configuration file>

In VMD (Tip: try also the new "Colvars Dashboard" plugin):

cv molid top
cv configfile <Colvars configuration file>

In LAMMPS:

fix Colvars all colvars configfile <Colvars configuration file>

In GROMACS:

gmx mdrun -s topol.tpr -deffnm topol -colvars <Colvars configuration file>

The contents of the configuration file are typically the same across all programs, for example:

colvar { # Define a new variable
  name d # Must give a name to this variable
  width 0.2 # Estimated fluctuation amplitude and/or grid resolution, "w_d"
  distance { # This variable is a distance between centers of mass (COMs)
    group1 { atomNumbers 1 2 3 } # List the atoms of the 1st group
    group2 { atomNumbers 4 5 6 } # List the atoms of the 2nd group
  }
}

harmonic { # Define a harmonic potential, 1/2*K*(d-d0)^2/w_d^2
  colvars d # Apply it to the variable "d"
  centers 5.0 # The center of the potential, "d0"
  forceConstant 10.0 # Force constant, "K"
}

Complete input decks for some of the most commonly used features are available in the examples repository: https://github.com/Colvars/examples

See also the examples folder of this repository for other examples of configurations. Configuration options (particularly, the selections of atoms) require minimal changes to reflect the specifics of each simulation.

The tests folder also contains functional segments of Colvars configuration, used to build numerical tests of code accuracy and stability. Feel free to use these segments in your production runs.

Updating to the latest version

To recompile each program with the most recent version of the module, download the master branch of this repository, or clone it via git:

git clone https://github.com/Colvars/colvars.git

and run the provided update-colvars-code.sh script against the unpacked source tree of any of the supported programs:

./update-colvars-code.sh /path/to/lammps           ; # updates LAMMPS
./update-colvars-code.sh /path/to/NAMD_X.YY_Source ; # updates NAMD
./update-colvars-code.sh /path/to/vmd-X.Y.Z        ; # updates VMD
./update-colvars-code.sh /path/to/vmd-plugins      ; # updates VMD plugins
./update-colvars-code.sh /path/to/gromacs-XXX.X    ; # update GROMACS

and recompile them.

The update-colvars-code.sh script support patching the latest development version of each program:

LAMMPS;
NAMD;
VMD and its plugins; note that starting from Colvars version 2023-06-23, some updates are needed to the VMD build script (see here for details).

For GROMACS, support for specific release series is currently maintained; pre-patched versions of specific releases are provided below.

All of the above MD engine versions are automatically tested as part of GitHub Actions workflows.

GROMACS-Colvars releases

The following links provide specific versions of GROMACS that are already patched with the latest available version of Colvars:

GROMACS 2022.4-colvars;
GROMACS 2021.6-colvars;

The Colvars patching procedure described earlier was used to produce the two patched GROMACS version. This procedure is generally compatible with all GROMACS versions within the same release year. Unless there is a specific reason not to, it is a good idea to use the latest revision of each release series, available as Git branches.

When posting a message to the Gromacs forum related to any Colvars-patched version of GROMACS please always specify "GROMACS modification: Yes" and use the colvars tag. Whenver possible please also reference the Colvars version: this is included in the version string that is reported by the patched GROMACS (right after the GROMACS version), for example:

   :-) GROMACS - gmx_d, 2021.5-Colvars-2022-02-20-dev (double precision) (-:

Which version of Colvars is recommended?

The Git master branch is to be considered the "stable" release at any given time; any bugfixes are released through master first. The input syntax is near-completely backward-compatible and output files are forward-compatible. Feel free to download Colvars and update NAMD, VMD, LAMMPS or GROMACS as needed.

Other branches are dedicated to the development of specific features: please use them at your own discretion.

Which version of Colvars is included in package XX version YY?

The specific version of Colvars is identified both in the code and in the documentation by the date of the most recent code revision (e.g. 2021-01-19). This date is printed to the standard output or log file as soon as Colvars is activated.

A table mapping software package release versions to Colvars versions is given here.

If you are using a stable release of any of the codes mentioned above, feel free to use the version number of that code when asking questions.

Feedback

Please use the "Issues" tab of this page to submit new bug reports or to suggest new features.

License

This software is distributed under the GNU Lesser General Public License (LGPL), version 3. See COPYING.LESSER for complete licensing terms.

In the interest of broad distribution, copies of this code are also distributed together with LAMMPS (LGPL version 2), NAMD and VMD (UIUC license). However, the terms of the LGPLv3 license still apply to code originating from this repository.

Colvars/colvars

Colvars

Reviews

Repository Details