Viparr is a set of tools and libraries for building forcefields for molecular systems suitable for molecular dynamics simulations. It requires the msys library, distributed by D.E. Shaw Research. Forcefield files for commonly used forcefields may be found in the D. E. Shaw Research viparr-ffpublic github repository.

Building Viparr

Building viparr requires that you have first built and installed msys; see the associated instructions. The lpsolve and InChI optional features are not required for viparr. Like msys, viparr requires Scons, a C++ build tool; numpy headers for each python version you want to support; and boost headers and libraries (filesystem, system, and program_options).

To build and install viparr, use the scons tool:

PYTHONPATH=external:$PYTHONPATH scons -j4 PYTHONVER=37 PREFIX=$HOME/local install

where PREFIX is the location of the msys installation.

Documentation for viparr is in sphinx format. To build the documentation, first install viparr, then run the following in the doc directory:

PYTHONPATH=$HOME/local/lib/python make clean html

Running Viparr

Fetch the forcefield files from the viparr-ffpublic repository, and set the environment variable VIPARR_FFPATH to the full path of the ff directory located within the viparr-ffpublic checkout. To parameterize, for example, a molecular system containing protein, lipids, water, and ions, using a set of Amber forcefields, specify the name of each forcefield directory as an argument to viparr:

viparr input.dms output.dms -f aa.amber.ff99SB-ILDN -f lipid.amber.lipid17 -f water.tip3p

If you have a viparr-compatible forcefield directory that isn't contained within viparr-ffpublic, you may specify it directly with the -d option.

Viparr is distributed with tools to convert forcefields from CHARMM and Amber formats.