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Desmond

Introduction

Desmond is a molecular dynamics simulation program for biomolecular systems.

Set Up

Before Desmond can be used, the appropriate module must be loaded:

module load desmond

Make a personal copy of the file scrodinger.hosts:

mkdir ~/.schrodinger
cp $SCHRODINGER/schodinger.hosts ~/.schrodinger

You should modify this to change the parameters passed to Slurm, e.g.

name:           localhost
schrodinger:    /cm/shared/apps/desmond/2012
tmpdir:         /scratch
env:            SCHRODINGER_RSH=/usr/bin/ssh
env:            SCHRODINGER_RCP=/usr/bin/scp
processors:     12

name:           main
host:           soroban
qargs:          --partition=main --ntasks=%NPROC% --mem-per-cpu=1024
processors:     1320
queue:          SLURM2.1

name:           test
host:           soroban
qargs:          --partition=test --ntasks=%NPROC% --mem-per-cpu=1024
processors:     36
queue:          SLURM2.1

name:           myMain
host:           soroban
qargs:          --partition=main --ntasks=%NPROC%   --mem-per-cpu=1024   --ntasks-per-node=1
processors:     1320
queue:          SLURM2.1

Submitting a batch job

Normally jobs are submitted using commands provided by the batch system. However, Desmond is started via a higher-level scripts instead. To run a Desmond job, create a file, say run001, similar to this example:

module load desmond/2012

$SCHRODINGER/utilities/multisim -HOST myMain -JOBNAME test42 -maxjob 1 -cpu 24  \
-m 1g3mpaps_MD.msj -c 1g3mpaps_MD.cfg -o 1g3mpaps_MD-out_42.cms 1g3mpaps_MD.cms \
-mode umbrella

This file must be executable (run chmod u+x run001 if necessary). Submit the job by calling

./run001

The value for the option -HOST must be the name of a stanza in the schrodinger.hosts file.

Monitoring jobs

Although the the usual Unix tools such as top and ps and the SLURM commands squeue, scontrol and sacct may be used for monitoring job, Desmond also provides jobcontrol, which is called via $SCHRODINGER/jobcontrol e.g.

$SCHRODINGER/jobcontrol -list all

The database, which consists of plain text files, for the jobs can be found in ~/.schrodinger/.jobdb2