applying experimental constraints to a MD simulation

From: L. Michel Espinoza-Fonseca (
Date: Sun Mar 11 2007 - 18:14:16 CDT

Hi all,

I was wondering if my specific problem can be solved with NAMD -I
really hope so. Right now, we have all this bunch of experimental data
(CA-CA distance distributions, to be more exact), and I'd like to use
them as "constraints" to build a 3-D model of a protein, using MD
simulations. I've used the harmonic constraints parameters included in
NAMD before, but usually you apply a force instead of a given
distribution of distances. Based on this, I'd like to know if any of
you have an idea on how to fit one (or multiple) distribution(s) of
distances (let's say, from 45 to 55 A) into the MD simulation. All
comments will be greatly appreciated!!!


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