Multisim Stage Plugins

MSJ, .msj

When running a molecular dynamics simulation, there are numerous different capabilities you may want to run, and different types of data you can extract. Desmond modularizes a significant amount of its functionality in the form of “plugins”, which allows you to choose the specific functionality you would like to execute.

A large number of plugins take in two keywords: first and interval. These specify the first timestep and the timestep interval at which the plugin should be applied, respectively. Plugins that write to a file also take in a name, which corresponds to the name of the file the plugin should be writing to.

Plugins that support a default configuration can be activated by specifying a “true”-style boolean (as specified in the ARK Syntax Guide) – most commonly plugin = on. This declares that the plugin should run, and use the default values. To configure plugins, you may specify a map of values instead of a boolean (like stages and other keywords).