VMD has the capability to work with a molecular dynamics program running on another computer, in order to display the results of a simulation as they are calculated; we refer to this capability as Interactive Molecular Dynamics (IMD). As new atomic coordinates are generated by the simulation process, they can be transferred directly over the network to VMD, which can then animate the molecule. A major feature in VMD is the ability to add perturbative steering forces to a running simulation, which are incorporated directly into the dynamics calculation.
In order for VMD to work in this fashion as a graphical front end and control console for a remote molecular dynamics simulation, it is necessary to have a version of a molecular dynamics program configured for IMD communication. The program NAMD, developed the the University of Illinois Theoretical Biophysics Group, will support IMD beginning with release 2.1. See the NAMD WWW home page for information on obtaining a copy of NAMD. NAMD is a parallel molecular dynamics program written in C++, which implements the CHARMM energy function. It is compatible with X-PLOR style PSF, PDB, and parameter files. The rest of the discussion in this chapter assumes you are using NAMD.