Running Desmond
There are two main, recommended ways to run a Desmond simulation:
- Through the GUI interface
- Through the
multisimworkflow manager
The first is done with Maestro, and prioritizes convenience by handling much of the default setup, but may make it harder to modify advanced settings. The second is extremely customizable, allowing users to modify all possible parameters and better control job launching, but requires technical knowledge of how to modify files and submit calculations from the command line.
In practice, a combination of the two methods may be used. It is quite common to use Maestro for system preparation and the generation of input configuration files (the MSJ file for multisim), but to then modify the default files and set up the calculation from the command line.
It is possible to run Desmond directly with the $SCHRODINGER/desmond command and providing the necessary input files. However, this only runs a single molecular dynamics simulation, and is not as robust to input errors. Most workflows involve a sequence of tasks and simulations, which is quite frustrating to set up without the tools mentioned above. As such, it is strongly recommended that Desmond jobs are run using either a Maestro panel, or multisim.
No matter the method, Desmond jobs are run under the Job Control facility, which manages the details of starting the job, transferring files, checking on status and so on. For more information about this facility and how it operates, as well as details of the Job Settings dialog box, see the Job Control Guide.
Click on a step below to learn more about how to perform the step using Maestro or the command line.
Molecular Dynamics with Desmond