**From:** Jerome Henin (*jhenin_at_cmm.chem.upenn.edu*)

**Date:** Fri Mar 16 2007 - 11:57:25 CDT

**Next message:**hl332_at_drexel.edu: "problem with namddat_unix: Plz help..."**Previous message:**L. Michel Espinoza-Fonseca: "applying experimental constraints to a MD simulation"**In reply to:**L. Michel Espinoza-Fonseca: "applying experimental constraints to a MD simulation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Michel,

If you apply a harmonic restraint on the distance with force constant k at

temperature T, you should get an approximate Gaussian distribution of width

sigma = sqrt( RT / k )

(it will be rigorously Gaussian if the restraint force is much stronger than

whatever coupling there is to other dgrees of freedom).

So there is no need to define an interval: you should be able to tune your

force constant directly based on the experimental dispersion.

Best,

Jerome

On Friday 16 March 2007 12:31, L. Michel Espinoza-Fonseca wrote:

*> Hi all,
*

*>
*

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

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

*> Then I won't have a real control on my distance distribution, is that
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*> correct? So I looked at the manual, and I found out that I can do the
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*> following:
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*>
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*> dist ( PEP1,6,ca) (PEP2,6,ca) kf=20 low=13.337 hi=8.337
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*>
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*> So the distances fluctuate within these two values. I'm not very
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*> familiar with this procedure, so I'd like to know if I'm correct. If
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*> not, I'm open for suggestions!!!
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*>
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*> Thanks!
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*> Michel
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*>
*

*> ORIGINAL POSTING:
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*>
*

*> Hi all,
*

*>
*

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

*> Thanks!
*

*> Michel
*

*>
*

*> 2007/3/12, Dan Bolintineanu <bolintineanu_at_cems.umn.edu>:
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*> > I think you can use the urestraint command, which is part of the free
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*> > energy calculation module. Something like:
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*> >
*

*> > freeEnergy on
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*> > freeEnergyConfig {
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*> > urestraint {
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*> > dist ( PEP1,6,ca) (PEP2,6,ca) kf=20 ref=13.337
*

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

*> > Good luck.
*

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