Multisim Stages
MSJ, .msj
Stages generally correspond to one subjob, or a set of related subjobs completing a single task. Not all stages launch a molecular dynamics simulation. The ones that do are considered members of the Desmond family of stages. Stages can run analysis scripts, modify output files from a previous stage, or prepare files for a later stage.
Click on a specific stage linked below for details on its functionality, keywords, and usage examples (when relevant). For keywords accepted by multiple stages, see General multisim Stage Keywords.
Note:
When discussing stage parameters, nested keywords can be represented both as a map (stage { parameter = { keyword } }) or using dotted (“pathname”) notation (stage.parameter.keyword). For more information on syntax, see ARK Syntax.
Click on a category below to filter stages by their high-level functionalities. These categories are noted in the
- All
- Workflow
- System Preparation
- Simulation/Desmond
- Structure Modification
- Analysis
- Materials Science
- FEP+
task—describes the type of jobanalysis—analyze MD simulation trajectoriesassign_custom_charge—assign charges to ligandsassign_forcefield—assign forcefield parametersaverage_cell—calculates average unit cell size and sets cell size to the resultbuild_geometry—prepare a model systemconcatenate—run multiple simulate stages as a single processdeform_cell—change the length of the system celldesmond_extend—extend a previous simulate stagedisordered_system_builder—creates a disordered system from the input structureextern—run arbitrary custom Python codeextract_solute_structures—extract solute structures from a previous simulationextract_structures—extract structures from an input.maefileextract_subsystem—create a new CMS file with a subsystemfep_analysis—analyze FEP+ simulationslambda_hopping—run a lambda hopping simulation on the systempl_analysis—analyze protein-ligand interactions in a simulation trajectoryreplica_exchange—run a replica exchange MD simulation on the systemreplicate_structure—replicate an output structure from a previous stage and copy its propertiesses_stage—scale nonbonded interactionssimulate—run an MD simulation on the systemsolvate_slab_builder—add solvent to slabsstop—stop the workflow at this stagetrim—remove unwanted stage data filesvrun—energy calculations on trajectories
Workflow
“Workflow” stages are those that do not necessarily perform simulation-relevant tasks, but instead help facilitate workflow management through multisim. These include the “task” and “stop” stage, which help define the workflow being run and whether to end a workflow early, respectively. Workflow stages can be very useful for advanced manipulation of stages and multisim workflows.
System Preparation
“System preparation” stages are used to set up a structure for a Desmond calculation. These stages can have a number of different functionalities, ranging from modifying the forcefield, adding system components to the input structure, or otherwise modifying the initial structure. System preparation stages are versatile, and can be run as their own workflow, or as part of a larger simulation.
Simulation/Desmond
These stages are ones that directly launch the Desmond engine for a simulation. They are generally either simulate stages, or implementations of this stage. For more details on configuring these, see the simulate stage.
Structure Modification
The “structure modification” tag for a stage is highly general. Stages of this type are ones that take in an input structure (either from the user, or a previous stage), and perform some sort of modification or extraction on that structure. Many of these stages write out a new structure, which can then be used by later stages.
Analysis
“Analysis” stages perform a variety of post-simulation functions and calculations, to help extract meaningful information from a system. This can include generating plots, extracting values from simulation data, or analyzing trajectories. Performing analysis in a multisim workflow can be a convenient way to receive immediate results following a simulation.
Materials Science
Schrodinger has an extensive suite of Materials Science tools aimed at supporting a variety of calculations and workflows. As mentioned in Synergy with the Schrodinger Suite, Desmond is a key part of various bulk property calculations, and other materials science tools. Stages that were either designed explicitly for Materials Science, or are predominantly used in MatSci workflows are tagged as such to easily identify them.
FEP+
FEP+, one of the most prominent workflows developed by Schrodinger, is built on the Desmond engine. There are a number of stages that were designed explicitly to support these calculations, and are usually of a secondary type as mentioned above (i.e. fep_analysis is an FEP+ stage, and an analysis stage).