Re: applying experimental constraints to a MD simulation

From: Mark Abraham (
Date: Sun Mar 11 2007 - 18:36:01 CDT

L. Michel Espinoza-Fonseca wrote:
> 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!!!

It sounds like you're wanting to build a structure from NMR constraints
- why not use the software that has been designed for that task? I've no
idea what NMR people use these days, though!

Be aware, though, that satisfying all of your constraints simultaneously
can lead to producing an unphysical structure... NOEs are derived from a
population of structures, and if there is significant disorder, then not
all members of the population are producing all of the NOEs all the time...


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