Desmond is a software package that perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. 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.
Availability and Restrictions
The Desmond package is available on Owens. The versions currently available at OSC are:
You can use
module spider desmond to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access for Academic Users
Desmond is available to not-for-profit OSC users; simply contact OSC Help to request the appropriate form for access.
Publisher/Vendor/Repository and License Type
D E Shaw Research, Non-Commercial
Usage on Owens
To set up your environment for desmond load one of its modulefiles:
module load desmond/2018.2
Desmond comes with Schrodinger interactive builder, Maestro. To run maestro, connect to OSC OnDemand and luanch a virtual desktop, either a Virtual Desktop Interface (VDI) or an Interactive HPC Desktop, and in desktop open a terminal and run:
Here is an example batch script that uses Desmond non-interactively via the batch system:
# Example Desmond single-node batch script. #PBS -N multisim-batch #PBS -j oe #PBS -m ae #PBS -l walltime=0:20:00 #PBS -l nodes=1:ppn=28 #PBS -S /bin/sh qstat -f $PBS_JOBID export module load desmond module list cd $PBS_O_WORKDIR pbsdcp -p 'desmond_md_job_butane.*' $TMPDIR cd $TMPDIR $SCHRODINGER/utilities/multisim -HOST localhost -maxjob 1 -cpu 24 -m desmond_md_job_butane.msj -c desmond_md_job_butane.cfg desmond_md_job_butane.cms -mode umbrella -ATTACHED -WAIT ls -l pbsdcp -p '*' $PBS_O_WORKDIR
The WAIT option forces the multisim command to wait until all tasks of the command are completed. This is necessary for PBS batch jobs to run effectively. The HOST option specifies how tasks are distributed over processors.