Viewing and Analyzing Desmond Simulations

Viewing Trajectories

You can view the trajectory from a Desmond simulation in Maestro with the Trajectory Player. To display the Trajectory Player, first import an output structure file (-out.cms) into the Workspace. Then, double-click the T button in the Title column of an entry in the Entry List or Project Table, or click this button and choose Load Trajectory.

You can also use PyMOL to view trajectories and create images and movies.

Analyzing Trajectories

There are several ways in which you can analyze Desmond simulations. Some analyses can be performed on any molecular dynamics simulation, others can only be performed on specific types of simulations.

• To play the trajectory as movie, extract snapshots, and perform interactive analysis, use the Trajectory Player.

  You can measure geometric and energy-based properties, such as RMSD, RMSF, hydrogen bonds, or Coulomb energy, as well as calculate radial distribution functions from the Plot button menu of the Trajectory Player.

• To cluster a trajectory, use the Trajectory Frame Clustering Panel.
• To check ensemble properties, such as potential energy, temperature, or pressure, use the Simulation Quality Analysis Panel.
• If you performed a molecular dynamics simulation of a protein-ligand system, use the Simulation Interactions Diagram Panel to analyze properties specific to protein-ligand systems.
• If you performed molecular dynamics calculations with the Materials Science suite, there are a variety of panels that can be used for analysis, listed under Tasks → Classical Mechanics → Trajectory Analysis.
• If you performed metadynamics simulations, you can analyze them with the Metadynamics Analysis Panel
• If you performed replica exchange simulations, analyze them with the Replica Exchange Dynamics Review Panel panel.

See Analyzing Desmond Simulations for information on analyzing trajectories from the command line.