applying experimental constraints to a MD simulation

From: L. Michel Espinoza-Fonseca (
Date: Fri Mar 16 2007 - 11:31:41 CDT

Hi all,

Below find my original posting. Dan suggested a very interesting
approach to my problem (restraining the distance between two atoms) by
using the free energy module of NAMD. The approach sounds interesting
and I think it can be potentially used to solve my problem. However, I
have one more question. I have a very specific distribution of
distances obtained from experiments (let's say, x +/- 2*stdev). Such
distribution accounts for 95 % of the population, based on our
Gaussian distributions. The problem here is that (If I'm right) if I
apply this:

dist ( PEP1,6,ca) (PEP2,6,ca) kf=20 ref=13.337

Then I won't have a real control on my distance distribution, is that
correct? So I looked at the manual, and I found out that I can do the

dist ( PEP1,6,ca) (PEP2,6,ca) kf=20 low=13.337 hi=8.337

So the distances fluctuate within these two values. I'm not very
familiar with this procedure, so I'd like to know if I'm correct. If
not, I'm open for suggestions!!!



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!!!


2007/3/12, Dan Bolintineanu <>:
> I think you can use the urestraint command, which is part of the free
> energy calculation module. Something like:
> freeEnergy on
> freeEnergyConfig {
> urestraint {
> dist ( PEP1,6,ca) (PEP2,6,ca) kf=20 ref=13.337
> dist ( PEP1,6,ca) (PEP2,8,ca) kf=20 ref=13.3244
> dist ( PEP1,6,ca) (PEP2,13,ca) kf=20 ref=9.65392
> }
> pmf {
> task = stop
> lambda = 1
> time = 260 ps
> }
> }
> Not to worry, this won't actually carry out free energy/pmf-type
> calculations, it's just the syntax required to make it do what you
> want. Change time to however long your simulation is (you'll need to
> specify numsteps > time somewhere else in the config file). kf is an
> effective force constant (the higher this is, the more rigid your
> constraint), and ref is the target restraint distance. The selection
> I have there is for atom-to-atom distance restraints (segid, resid,
> atom name), but you can do much more sophisticated ones
> (centre-of-mass to centre-of-mass, angles, etc.). See "Options for
> confromational restraints" in the manual (in my version, it's section
> 6.7.3).
> Good luck.

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