A virtual environment for steered molecular dynamics

A molecular dynamics simulation approximates the motion of atoms in a system of molecules over short intervals of simulated time, typically on the order of picoseconds to nanoseconds. Such simulations may run for days or weeks on a computer when used to investigate the dynamic behavior of small proteins in biological systems. By adding additional restraints, a simulation may be “steered” to observe the possibility of particular behaviors or to eliminate others over shorter timescales. We have developed the Steered Molecular Dynamics (SMD) system to interactively place and observe the effects of restraints in a running dynamics simulation. In this article we describe an application of SMD to the extraction of small ligands from proteins, and an immersive virtual 3D environment through which the SMD system can be operated. The virtual environment is constructed using the Protein Interactive Theater (PIT) system, a head-tracked stereo workspace for two users.