Article ID: 820 - Last Modified: December 4, 2010
Do I have to center my MD trajectory before I can visualize it?
No, you don't need to run any postprocessing calculations before you can have a look at your trajectory. By default in Desmond the "Glue close solute molecules together" option is selected, which has no effect on the physics of the trajectory but avoids the problem that associated solutes are displayed on opposite sides of the simulation box. Additionally in the Trajectory Viewer panel there is an option to superimpose molecules based on a certain reference frame or to center them on the fly.
Keywords: Desmond, trajectory, Maestro, MD
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