DESMOND

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer. Desmond includes code optimized for machines with an NVIDIA GPU.

Sample scripts for Desmond use are available in directory /opt/packages/examples/desmond on Bridges.

Documentation

• See the Desmond documentation at https://www.deshawresearch.com/resources_desmond.html
• Citation: to cite Desmond in a publication, use this paper, which won the “Best Paper Award” at the 2006 ACM/IEEE Conference on Supercomputing (SC06).

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw, “Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,” Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006. Text

Usage 

To see what versions of Desmond are available type

module avail desmond

To see what other modules are needed, what commands are available and how to get additional help type

module help desmond

To use Desmond, include a command like this in your batch script or interactive session to load the desmond module:

module load desmond

Be sure you also load any other modules needed, as listed by the module help desmond command.