OpenMM Code Repository
The Code Repository contains a list of the many additional files and software that can be used with OpenMM to enhance its capabilities. The OpenMM team has reviewed the links on this page. We also encourage the community to add their own contributions here.
Title/Description | Author/Team | Date Added to/Updated in Cookbook
(optional: extended 2-3 line description)
Tutorials
Tools
OpenMM Script Builder | Robert McGibbon | 5/09/2013
- A web application to generate scripts for running OpenMM simulations. Includes pull-down menus, pop-up tips, error checking, and live script building capabilities.
Simulated Tempering | Peter Eastman | 7/29/2015
- An implementation of simulated tempering, an accelerated sampling method that jumps between temperatures to allow barriers to be crossed more easily.
PLUMED Plugin | Peter Eastman | 3/18/2016
A plugin that connects OpenMM to PLUMED, a code for collective variables. It allows you to define collective variables in PLUMED, then apply forces to an OpenMM simulation based on them.
Rigid Bodies | Peter Eastman | 8/30/2016
- A script for performing rigid body simulations.
Molecular dynamics script and energy/force validation module | Lee-Ping Wang | 12/04/2012
- OpenMM-MD.py is a general purpose script (with lots of comments) that uses the OpenMM Python module to drive MD simulations. Simulation options are handled via an input file. To facilitate use of the script, the available options are always printed out for you to see, along with documentation.
- tinker_reporter.py contains a Reporter class which calls TINKER to validate the energies and forces from OpenMM. This requires a TINKER simulation to be set up in parallel with the OpenMM simulation.
Multiple time step integrator | Peter Eastman | 4/30/2013
- [This script is bundled with OpenMM in versions 6.3 and later.] An implementation of the rRESPA multiple time stepping algorithm. This allows different forces to be evaluated at different frequencies so that quickly changing, inexpensive forces are computed more often than slowly changing, expensive ones.
aMD integrators | Peter Eastman and Steffen Lindert | 3/29/2013
- [This script is bundled with OpenMM in versions 6.3 and later.] A set of integrators for performing aMD, an accelerated sampling method that modifies the energy surface to increase the rate of transitions.
PME optimizer | Peter Eastman | 10/8/2013
- A script to optimize the performance of PME. It runs a series of simulations and selects the parameters that give best performance for simulating a particular system on particular hardware.
OpenMM-Enabled Applications
GROMACS | OpenMM Team | 11/30/2012 .
- GROMACS is a molecular dynamics package led by Erik Lindahl and Berk Hess of the Stockholm Center for Biomembrane Research and David van der Spoel of the University of Uppsala in Sweden. It is written in C.
CHARMM | Michael Garrahan and Charles Brooks | 11/30/2012
- CHARMM is a molecular dynamics package written in FORTRAN77 with contributors from around the world.
TINKER | OpenMM Team | 11/30/2012
- TINKER is a molecular dynamics package from Jay Ponder's lab with some special features for biopolymers.
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