Multisim

MSJ, .msj

A typical Desmond workflow involves multiple molecular dynamics (MD) simulations corresponding to different tasks such as setup, equilibration, and production. Desmond uses multisim as a workflow manager to facilitate running these tasks (known as “stages”) in an efficient, user-friendly way. Workflows are defined through multisim configuration files (.msj), which detail each Desmond “stage” the workflow should run in order, along with the relevant parameters for each stage.

Stages perform a variety of tasks, as detailed in Multisim Stages, and each stage contains its own set of configurable parameters. This allows for the creation of completely custom workflows, with multisim handling the configuration and execution of the actual jobs.

This chapter walks through the workflow execution capabilities of multisim first, allowing users to immediately get set up with launching Desmond jobs. The rest of the sections involve descriptions of each stage, including a description of its functionality along with some of the configurable parameters that stage accepts.

See the following topics to learn about the workflow execution capabilities of multisim:

• Running Simulations with multisim
• Restarting multisim Jobs
• Extending multisim Jobs

For information on the multisim configuration file and the stages that you can define there, see:

• Multisim Configuration (MSJ) Files
• Multisim Stages