Subject: Re: CCL:movie of docking

From: Richard Gillilan <[email-masked]>
Date: Fri, 24 May 2002 08:50:19 -0400

Docking problems are small enough that
you could possibly run a single trajectory
and wait long enough to actually see a docking
occur. This is after all how simulated annealing
works. But you will waste a lot of time waiting
for this to happen ... it will be a rare event.
The easier thing to do is to run a trajectory
in reverse starting in a docked configuration. 
Hamiltonian dynamics is time-reversible so the 
undocking trjectory is simply a docking trajectory
with the signs of the momenta (or time) reversed.
This trick has been used for years.

Any number of simulation programs will probably
work for this purpose.

Richard Gillilan
MacCHESS, Cornell