Desmond

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

Installed on: blacklight.

Usage:

1. Create a batch job containing commands to:
   • Set up the module command.
   • Load the boost module

     module load boost

   • Load the Desmond module

   module load desmond

   • Run desmond

     mpirun -np  $PBS_NCPUS dplace -s1 desmond    --include config-file --cfg configuration options  --destrier mpi 

     where:

     dplace

     is used to bind a set of processes to specific nodes to minimize memory accesses to other nodes. See man dplace for more information.

     --destrier mpi

     is used to run desmond in parallel. Without this flag, desmond defaults to serial.

     See the Desmond documentation for a complete description of configuration files and options.

2. Submit the job using the qsub command.

Example job

See a sample job.

Notes

To enable a built-in plugin, you must include it in the list of plugins within the mdsim scope in the configuration file. For example:

mdsim{
  plugins=[status eneseq trajectory]
....
}

enables the following plugins.

status

records simulation time per unit of wall clock time, and reports a cumulative speed at the end

eneseq

records temperature, pressure, and other summary data

trajectory

records trajectory data

The options for each plugin should also be defined within the mdsim scope. For example:

 trajectory={
    first         =0
    interval      =0.5
    outdir        =trajectory
  }

defines the initial time and interval for the trajectory readings.

For a complete list of plugins supplied with Desmond and the available options, see the Desmond User's Guide.