This page provides resources to help you get started with molecular dynamics simulations.
Background Material
Slides and videos introducing molecular dynamics, given by Prof. Vijay Pande
Slides and videos on more advanced topics in molecular dynamics, given by Prof. Vijay Pande
Running Molecular Dynamics Using OpenMM - What Do I Download?
OpenMM is a library meant for developers to integrate into their molecular dynamics (MD) code. We have provided a number of applications built on top of OpenMM for the researcher to download.
OpenMM version of GROMACS: You can download and install the OpenMM version of GROMACS. GROMACS is one popular MD code developed by Erik Lindahl and his group. It is easiest to install on Linux and OS X platforms, and has a command-line interface. Simbios has provided modified files that enable GROMACS to run on GPUs. This is the OpenMM version of it. To install the OpenMM version of GROMACS, go to http://simtk.org/home/openmm. Click on Downloads and scroll down to the second section, titled OpenMM-Accelerated GROMACS. Follow the directions there.
OpenMM Zephyr: Simbios has also developed a GUI-version of the OpenMM version of GROMACS, called OpenMM Zephyr. This is available on Windows, Mac OSX, and Linux (beta version). It’s a good way to get started fast, but you won’t have access to as many of the simulation parameters. A compromise we’ve suggested is to generate the starting files with OpenMM Zephyr. Then tweak parameters within the starting files generated and run the simulations from the command-line.
OpenMM Zephyr can be downloaded from http://simtk.org/home/zephyr, as well as a tutorial on using Zephyr with the command-line (OpenMM/mdrun).