Running Simulations with multisim

Multisim offers a number of features that offer better integration with Desmond. Most important of these is the ability to easily run multi-stage workflows from the command line. Key to this is the MSJ file: the configuration file for multisim that specifies simulation details.

See the Overview of Desmond Simulations for background on the simulations being run. Particularly important is the need for a well-prepared structure. All commands below assume either a prepared structure file, or an MSJ which contains the appropriate stages to prepare the structure.

As is the case for all Schrödinger software, the environment variable SCHRODINGER must be set to the directory where the Schrödinger software, including Desmond, was installed. In addition, there are other environment variables that can be set to override default resource values.

Multisim jobs are by default executed in a node-locked mode (denoted by -mode umbrella), meaning only the main job is submitted to the queueing system, and all subjobs are run on the nodes allocated to the main job. This enables all stages of a multisim workflow to finish before new multisim jobs are scheduled to run. As the multisim process is not resource intensive, this does not lower the performance.

The basic syntax for the multisim utility is:

$SCHRODINGER/utilities/multisim [options] structure-file -m msj-file
$SCHRODINGER/utilities/multisim [options] -RESTART checkpoint-file

The first syntax should be used for new jobs, and the second for restarting jobs. The structure file can be either a Maestro (.mae) file or a Desmond CMS (.cms) file.

For a more advanced, multi-stage molecular dynamics workflow, the command would more closely resemble:

$SCHRODINGER/utilities/multisim -JOBNAME multistage -HOST mycluster\
                                -m input.msj -c input.cfg input.cms \
                                -o desmond-out.cms -mode umbrella \
                                -set stage[1].set_family.md.jlaunch_opt=["-gpu"]

which submits a multisim workflow with the jobname multistage to the remote host mycluster. The stages are defined in the multsim job file input.msj and the structure is provided in the Desmond CMS file input.cms. The default Desmond configuration parameters for all stages are read from input.cfg. The final structure will be written to desmond-out.cms. Multisim can run in node-locked or umbrella mode and launches the Desmond stages to a GPU.

For information on the command options, run the command with the -h option or see the multisim Command Help topic.