Molecular Dynamics in the Materials Science Suite

The following features for general MD simulations are specifically designed for the Materials Science Suite:

• Disordered System Builder — build a multicomponent system that is randomly distributed in a simulation box (Disordered System Builder Panel, Enumerate Disordered Systems Panel)

• Prepare for MD — convert a structure in the Workspace to a Desmond model system ready for simulation (Prepare for MD Panel)

• MD Multistage Workflow — run an MD simulation that consists of optional relaxation and multiple stages of minimization, molecular dynamics, simulated annealing, and other MD stages. (MD Multistage Workflow Panel)

• MS MD Trajectory Analysis — analyze a trajectory from a Desmond MD simulation and present information on bulk properties derived from the trajectory (MS MD Trajectory Analysis Panel)

• Coarse Grained Modeling — prepare a coarse-grained model system from an all-atom structure and define the force field for the coarse-grained particles (Coarse-Grained Modeling in the Materials Science Suite)

Other panels make use of MD simulations with Desmond for specific purposes, such as for bulk properties. The remaining molecular dynamics capabilities that are relevant for Materials Science are described in the User Manual.

For all-atom MD simulations, a custom version of the OPLS4 force field can be requested when you create the model system. The location of this force field is set in the Force Field settings section of the Preferences Panel. When you submit any kind of MD simulation job, the custom force field used is the one that is currently set in the Preferences Panel, which might not be the one that was set when the model system was built. However, this behavior allows you to change the path and re-run a simulation with a different custom force field, to examine the effects of the customization.