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:
- 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.
- 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.
