Getting started with MD simulations

GROMACS is another commonly used MD simulation engines and can be downloaded for free here, but there are many more like LAMMPS, etc.

PyMOL is another commonly used MD simulation visualization programs (other than VMD) and can be downloaded for free here (college students). Chimera X is also a great visualization program.

How to set up MD simulations (taken from

Protein structures from various structural determination methods often are not complete. For example, structures from X-ray crystallography typically do not have resolved hydrogens. Given the importance of hydrogen bonding, which requires hydrogen participation, for protein stability and receptor-ligand interactions, X-ray crystal structures cannot be used used in molecular dynamics (MD) right “off the shelf.” 

Please refer here for example Amber scripts.

Great introductory slides on MD and WE by Prof. Matthew Zwier!


WE Review Paper: Zuckerman, Daniel M., and Lillian T. Chong. "Weighted ensemble simulation: review of methodology, applications, and software." Annual review of biophysics 46 (2017): 43.

WESTPA 2.0: Russo, John D., et al. "WESTPA 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications." Journal of Chemical Theory and Computation 18.2 (2022): 638-649.

WESTPA 1.0 (older version but still has a valuable overview of the WESTPA program): Bogetti, Anthony T., et al. "A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]." Living journal of computational molecular science 1.2 (2019). 

GaMD: Miao, Yinglong, Victoria A. Feher, and J. Andrew McCammon. "Gaussian accelerated molecular dynamics: unconstrained enhanced sampling and free energy calculation." Journal of chemical theory and computation 11.8 (2015): 3584-3595.

An example of how WE is able to sample biologically relevant timescales

Download the latest WESTPA here for your workstation and supercomputer cluster

Installation for PowerPC architecture, etc. (alternative installations) can be found here

Checklist for WESTPA simulation

Using the HDF5 trajectory storage scheme

Minimal adaptive binning scheme video

WESTPA tutorials

Q&A forum for WESTPA 

How west.h5 is structured

Getting thermodynamic and kinetic properties from WESTPA simulations