Composite Model System (CMS) Files

Composite model system (CMS) files are multi-structure Maestro files that are suitable for initiating MD simulations with Desmond. The prepared model system may contain up to six components, each of which is stored as a separate entry in the CMS file:

• Full system
• Solute (typically contains protein-ligand complex)
• Membrane (for lipid-containing systems)
• Positive Ions
• Negative Ions
• Water

The CMS file may also contain force-field parameters, which can be assigned by the System Builder Panel or assign_forcefield stage in a Multisim job.

In a Desmond calculation, one will find two kinds of CMS files: “-in.cms” and “-out.cms”. The input CMS file is usually the output of some kind of Desmond system preparation (i.e. the build_geometry stage or the System Builder Panel), and represents a valid MD system without an associated trajectory. The output CMS file is generated by the Desmond simulation, and is in most ways identical to the -in.cms. However, these files contain an associated trajectory. While the trajectory itself is not stored in the -out.cms file, the relative path to the trajectory data is (within a structure-level property). If you are only supplying the CMS file to an analysis script or panel, it is important that the trajectory data is located in the same directory so that it may be referenced.

CMS files can be read by Maestro in the usual way, and the extra force-field data is read in as well as the structures. These entries in Maestro can be used as input to Desmond simulations, either using the Desmond panels for performing just the MD simulations (Molecular Dynamics Panel, Simulated Annealing Panel, Replica Exchange Panel, Metadynamics Panel), or the Materials Science application panels, for which the simulations are used to calculate properties of systems.