adding specific forces between atoms

From: Michael Zimmermann (
Date: Mon Sep 21 2009 - 15:44:48 CDT

Dear NAMD community,

I am setting up a type of flexible docking using simulated annealing.
We have some cross linking distances, so I was going to perform
simulated annealing on an initial docked conformation of two proteins
and place forces between the lysines that cross linked to pull them
together. The simulated annealing would then refine the joining of
the two proteins into a feasible conformation. My question is, how do
I add new interactions? It would be nice if there was something like
the consForceFile where I could designate "connect atom1 to atom2 with
harmonic force F1." tMD requires a known target conformation, sMD
could be used I suppose but it is not a straightforward (in my
opinion) implementation of it, AFB could be used to measure properties
of the interaction, but does not seem to be the addition of user
defined forces, tclforces is only documented (that I see) to add a
constant linear or rotational force.

Ideally, what I want is to be able to add a force to my system that
connects two atoms and reaches a minimum energy when the two atoms are
about 6 angstroms apart.

Thank you,

Mike Z

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