Pittsburgh Supercomputing Center 

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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
  2. 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.

  3. Submit the job using the qsub command.

Notes

For a complete list of plugins, see the Desmond Users's Guide.

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.

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