Desmond is a software package developed at D. E. Shaw research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. 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.

To run this software interactively in a Linux environment run the commands:

module load desmond

Input can be prepared and jobs launched from Maestro.

Note: do not load the schrodinger module; if you load that one, the desmond module will not work. If you load the schrodinger module in your .bashrc file, you will need to unload the module first:

module unload schrodinger


There are two distinctly different version of Desmond. The common version is distributed in binary form from D.E. Shaw and is bundled with Maestro. A second version is available on Itasca. This version is built from source and links many system libraries, resulting in a code that can scale to thousands of processors for some inputs. This build doesn't contain Maestro or many of the analysis features in the binary-distributed version. This 'from source' build is the default on Itasca, although the GUI enabled Maestro version can be loaded as well (desmond/2010-01).

The following is a pbs script that will run the apoa1 benchmark using Desmond on Itasca.
#!/bin/bash -l

#PBS -l walltime=01:00:00,pmem=500MB,nodes=256:ppn=8
#PBS -m abe


module load desmond/

orterun -np 1024 mdsim --include apoa1.cfg --cfg \
boot.file=apoa1.dms --destrier mpi > apoa1.1024.log

Additional Information

Help and tutorials are available by selecting the "Help" menu within Maestro.


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