Desmond Configuration (CFG) Files

config, cfg

The Desmond engine takes in .cfg configuration files, which specify the parameters of the molecular dynamics job. These parameters specify the conditions and nature of the simulation. They include values such as total time, temperature, and pressure, as well as details surrounding plugins to run and forces to apply.

Often, a distinction is made between the “frontend” and “backend” CFG file. The “frontend” CFG is the input to the Desmond engine, and mostly consists of user-set parameters. Desmond reads this, and before running a simulation, writes a “backend” cfg (usually ending with -out.cfg). This output CFG contains the full set of parameters used by the calculation (including Desmond-set defaults), and can be helpful in debugging. It also contains the input CFG at the top of the file, under the ORIG_CFG parameter. The Ark syntax from D. E. Shaw Research is used for both the back-end and front-end config files.

The input .cfg file is separate from the .msj file (Multisim’s configuration file), and is the only input configuration accepted by the Desmond backend (i.e. directly running $SCHRODINGER/desmond).