Package: colvars
# 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).The module itself implements a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.## Obtaining and usingThe easiest way to obtain binary versions of Colvars is via the simulation programs [NAMD](http://www.ks.uiuc.edu/Research/namd/) and [LAMMPS](http://lammps.sandia.gov/) and the visualization program [VMD](http://www.ks.uiuc.edu/Research/vmd/).  Please check [here](https://github.com/colvars/colvars/releases) to see which version of Colvars is included with the round-number versions of VMD and NAMD.  Colvars is integrated with LAMMPS on a near-continuous basis, most often immediately after significant code changes.## DocumentationThe [Colvars webpage](http://colvars.github.io/) includes user documentation for the three codes, as well as a Doxygen-based [developer documentation](http://colvars.github.io/doxygen/html/).The reference article is:G. Fiorin, M. L. Klein, and J. Hénin, Molecular Physics 111, 3345 (2013).http://dx.doi.org/10.1080/00268976.2013.813594  \[[BibTex file](https://github.com/colvars/colvars/blob/master/doc/ref_Fiorin_2013.bib?raw=true)\] \[[Endnote file](https://github.com/colvars/colvars/blob/master/doc/ref_Fiorin_2013.ciw?raw=true)\]## Example inputColvars requires a configuration file, or alternatively configuration arguments given through scripting commands by the linked program.  In NAMD:```colvars oncv configfile <Colvars configuration file>```In VMD:```cv molid topcv configfile <Colvars configuration file>```In LAMMPS:```fix Colvars all colvars configfile <Colvars configuration file>```The contents of the configuration file are typically the same across all programs, for example:```colvar { # Define a new variablename d # Must give a name to this variablewidth 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 groupgroup2 { atomNumbers 4 5 6 } # List the atoms of the 2nd group}}harmonic { # Define a harmonic potential, 1/2*K*(d-d0)^2/w_d^2colvars d # Apply it to the variable "d"centers 5.0 # The center of the potential, "d0"forceConstant 10.0 # Force constant, "K"}```Please see the [examples](https://github.com/colvars/colvars/tree/master/examples?raw=true) folder of this repository.  Configuration options (particularly, the selections of atoms) require minimal changes to reflect the specifics of each simulation.The [tests](https://github.com/colvars/colvars/tree/master/tests?raw=true) 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 versionTo recompile each program with the most recent version of the module, [download](https://github.com/colvars/colvars/archive/master.zip) 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/NAMD_X.YY_Source ; # updates NAMD./update-colvars-code.sh /path/to/vmd-X.Y.Z        ; # updates VMD./update-colvars-code.sh /path/to/lammps           ; # updates LAMMPS```and recompile them.The `update-colvars-code.sh` script is synchronized with the latest version of each program: [NAMD nightly build](http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD), [VMD CVS](http://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html) and the Github repository of [LAMMPS](https://github.com/lammps/lammps).  Earlier versions are not supported.## Which version is recommended?All bugfixes are released through the `master` branch, which is to be considered the "*stable*" release at any given time.  The input syntax is *backward-compatible* and output files are *forward-compatible*.  Feel free to download Colvars and update NAMD, VMD or LAMMPS as needed.Other branches are dedicated to the development of specific features: please use them at your own discretion.## FeedbackPlease use the "Issues" tab of this page to submit new bug reports or to suggest new features.## LicenseThis software is distributed under the GNU Lesser General Public License, version 3.  See COPYING.LESSER for complete licensing terms.