Desmond

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems.

Licensing and Access

To obtain access to the Desmond software module, please submit a request via SAFE confirming that you agree to the Desmond user license.

Running

To run Desmond you need to add the correct module to your environment.

Desmond

The default version of Desmond on ARCHER is currently 3.6.1.1, so

module add desmond

will give you access to desmond v3.6.1.1

Example Job Submission Script

The desmond job should be run from the directory in which the input files are stored. Below is an example job submission script adapted from that used to perform the parallel test specified by the files included with the Desmond distribution. This example uses just two cores from one node: each ARCHER node has 24 cores.

#!/bin/bash --login
#PBS -N des_job

#PBS -l select=1
#PBS -l walltime=1:0:0

# Replace this with your budget code
#PBS -A budget

# Move to directory that script was submitted from
export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
cd $PBS_O_WORKDIR

module add desmond

# This prevents any system libraries from using threading
export OMP_NUM_THREADS=1

aprun -n 2 desmond \
      --include ./share/samples/dhfr.cfg \
      --cfg boot.file=./share/samples/dhfr.dms \
      --cfg mdsim.plugin.eneseq.name=dhfr.eneseq \
      --destrier mpi

Compiling Desmond