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.


  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 


    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.


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:

  plugins=[status eneseq trajectory]

enables the following plugins.

records simulation time per unit of wall clock time, and reports a cumulative speed at the end
records temperature, pressure, and other summary data
records trajectory data

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

    first         =0
    interval      =0.5
    outdir        =trajectory

defines the initial time and interval for the trajectory readings.