AutoIMD is a means of quickly starting a NAMD molecular dynamics simulations
from atomic coordinates in VMD. The simulation can then be visualized in
real-time on the VMD graphics screen. With the appropriate devices
(such as a VRPN tracker), the user can also interact with a running
simulation and apply forces to individual atoms or residues.
Such an interaction is extremely useful when building and modeling systems,
and can also be used to gain precious insights by tinkering with key residues
Documentation and Tutorials