{
    "info": {
        "author": "Giacomo Fiorin",
        "author_email": "giacomo.fiorin@gmail.com",
        "bugtrack_url": null,
        "classifiers": [],
        "description": "# Collective variables module (Colvars)\n\nA 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).\n\nThe module itself implements a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.\n\n## Obtaining and using\n\nThe 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.\n\n## Documentation\n\nThe [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/).\n\nThe reference article is:\nG. Fiorin, M. L. Klein, and J. H\u00e9nin, Molecular Physics 111, 3345 (2013).  \nhttp://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)\\]\n\n## Example input\n\nColvars requires a configuration file, or alternatively configuration arguments given through scripting commands by the linked program.  In NAMD:\n```\ncolvars on\ncv configfile <Colvars configuration file>\n```\nIn VMD:\n```\ncv molid top\ncv configfile <Colvars configuration file>\n```\nIn LAMMPS:\n```\nfix Colvars all colvars configfile <Colvars configuration file>\n```\nThe contents of the configuration file are typically the same across all programs, for example:\n```\ncolvar { # Define a new variable\n  name d # Must give a name to this variable\n  width 0.2 # Estimated fluctuation amplitude and/or grid resolution, \"w_d\"\n  distance { # This variable is a distance between centers of mass (COMs)\n    group1 { atomNumbers 1 2 3 } # List the atoms of the 1st group\n    group2 { atomNumbers 4 5 6 } # List the atoms of the 2nd group\n  }\n}\n\nharmonic { # Define a harmonic potential, 1/2*K*(d-d0)^2/w_d^2\n  colvars d # Apply it to the variable \"d\"\n  centers 5.0 # The center of the potential, \"d0\"\n  forceConstant 10.0 # Force constant, \"K\"\n}\n```\n\nPlease 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.\n\nThe [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.\n\n## Updating to the latest version\n\nTo 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:\n```\ngit clone https://github.com/colvars/colvars.git\n```\nand run the provided `update-colvars-code.sh` script against the unpacked source tree of any of the supported programs:\n```\n./update-colvars-code.sh /path/to/NAMD_X.YY_Source ; # updates NAMD\n./update-colvars-code.sh /path/to/vmd-X.Y.Z        ; # updates VMD\n./update-colvars-code.sh /path/to/lammps           ; # updates LAMMPS\n```\nand recompile them.\n\nThe `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.\n\n## Which version is recommended?\n\nAll 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.\n\nOther branches are dedicated to the development of specific features: please use them at your own discretion.\n\n## Feedback\n\nPlease use the \"Issues\" tab of this page to submit new bug reports or to suggest new features.\n\n## License\n\nThis software is distributed under the GNU Lesser General Public License, version 3.  See COPYING.LESSER for complete licensing terms.",
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        "home_page": "http://colvars.github.io",
        "keywords": null,
        "license": "GNU Lesser General Public License version 3",
        "maintainer": null,
        "maintainer_email": null,
        "name": "colvars",
        "package_url": "https://pypi.org/project/colvars/",
        "platform": "UNKNOWN",
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        "project_urls": {
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            "Homepage": "http://colvars.github.io"
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        "requires_python": null,
        "summary": "Collective variables module for molecular simulation and analysis programs",
        "version": "0.1"
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