MD packages

This post lists several software packages and tools that are useful in molecular simulations.

MD simulation packages

1. OpenMM: a high-performance toolkit for molecular simulation. A nice OpenMM tutorial is here.

   • OpenMM PLUMED plugin: OpenMM plugin that provides connection between OpenMM and PLUMED.

   • OpenMM PyTorch plugin: OpenMM plugin to define forces with neural networks.

   • OpenMMTools: a Python library layer that sits on top of OpenMM. It implements various sampling methods, such as MCMC samplers, parallel tempering. This package is still under development!

2. NAMD : code | tutorial | user guide | mail list | performance tuning 1, 2 | benchmark

   psfgen: vmd plugin to build psf file that is needed to run MD simulations with NAMD.

3. Gromacs : Official manual | Tutorial 1, 2, 3, 4 | Performance tuning

Libraries that implement enhanced-sampling methods

1. PLUMED: plugin for molecular dynamics which provides a wide range of enhanced-sampling methods.

2. Colvars: library which implements MD sampling methods based on collective variables.

Visualization and analysis tools

• VMD : code | scripts | plugins | representations | docs

• MDAnalaysis: tutorial 1, 2

• MDTraj

• pytraj

• nglview: Jupyter widget to view molecular structures and trajectories.