General Description

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.

Basic Usage

A sample Desmond submission script is as follows:


#$ -M	# 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  

Further information

Visit the official website: [1]