Running Desmond Simulations from Maestro

The Desmond panels enable you to set up and run the main tasks available with Desmond: molecular dynamics, minimization, simulated annealing, replica exchange, and metadynamics jobs. The panels are designed to make setting up these types of jobs as easy as possible, and provide the most common simulation controls. The default values provided in the panels represent a good balance between accuracy and performance, and are adequate for most jobs without change. For more control over the simulation parameters, you can make settings in the Desmond — Advanced Options Dialog Box. Customized force fields can be used in a simulation; the location of an existing custom force field is set in the Preferences Panel. The Desmond panels (and related tools) are available from the Task Tool under Classical Simulation; the trajectory viewer is opened from the Project Table using the output entry for a job.

In addition to setting up simulations, you can use these panels to restart a simulation from a checkpoint file as generated by a previously interrupted simulation. In this situation, the panel enters a read-only state, in which most of the controls are set by the information read and cannot be changed.

You can restart or extend a simulation with the same parameters and number of processors using the checkpoint file saved at the end of the simulation. See Restart or extend a single stage of a Desmond simulation from Maestro for details.

All jobs run from these panels require a model system to be built first, in the System Builder Panel—see Building a Model System for Desmond Simulations for details.

Desmond simulations are run on a single graphics processor (GPU). The GPU is chosen automatically by the job driver, if the host has more than one GPU. Only one GPU can be selected for a simulation because the scaling with more than one GPU is poor. Requirements for the graphics processor are listed in the System Requirements. You must also set up the hosts file to identify the GPUs on hosts that have suitable graphics processors, with the gpgpu setting—see The Hosts File for information. There are also several Knowledge Base articles on GPU use for Desmond.

For details on individual panels, see the help topic for the panel:

The basic outline of a Desmond simulation as run from Maestro is as follows:

  1. Import the structure file for the system of interest into Maestro.

  2. Prepare the structure for simulation with the Protein Preparation Wizard. This step involves removing ions and molecules (which are artifacts of crystallization), setting correct bond orders, adding hydrogens, filling in missing side chains or whole residues as necessary, reorienting various groups and varying residue protonation states to optimize the hydrogen bonding network, and then checking the structure carefully.

  3. If your system is a membrane protein, embed the protein in the membrane. This step and the next two steps are performed in the System Builder panel.

  4. Generate a solvated system for simulation.

  5. Distribute positive or negative counter ions to neutralize the system, and introduce additional ions to set the desired ionic strength (when necessary).

  6. Relax the system either by minimization or by selecting the panel option to relax the model system before simulation.

  7. Set the simulation parameters in one of the general Desmond panels, for molecular dynamics, simulated annealing, or replica exchange.

  8. Run the simulation.

  9. Analyze your results using the Trajectory Viewer and other analysis tools.

Note: Although you can prepare and submit Desmond jobs from Windows and Mac hosts, you can only run them on Linux hosts.

For other applications which run Desmond in the backend, see Introduction to Desmond.