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.
A sample Desmond submission script is as follows:
#!/bin/csh #$ -M firstname.lastname@example.org # Email address for job notification #$ -m bea # Send mail when job begins, ends and aborts #$ -pe smp 8 # Specify parallel environment and legal core size #$ -q long # Specify queue #$ -N job_name # Specify job name module load desmond # Required modules desmond -P $NSLOTS -c desmond_md_job.cfg -in desmond_md_job.cms
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