Interactive Molecular Dynamics Interactive Molecule Dynamics (IMD) facilitates a direct communcation between VMD and a molecular dynamics program, e.g. NAMD. The primary purpose of this link is to allow users to send forces to atoms or groups of atoms in a running simulation, and allow the simulation to efficiently send coordinates back to VMD for display. IMD can be performed with a mouse interface, but excels when performed with a haptic device for interactive force feedback.

Gramicidin A

Gramacidin A Click on the thumbnail for an image of using IMD to study the gramicidin A system. In this study, a haptic device is used to pull a sodium ion through the channel formed in the lipid membrane by the protein. Analysis of the applied force gives information about the potential energy profile in the channel.

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Step-by-step instructions for performing IMD.

The technical details of IMD.