**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
*

*> 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
*

*> following:
*

*>
*

*> 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!!!
*

*>
*

*> Thanks!
*

*> Michel
*

*>
*

*> ORIGINAL POSTING:
*

*>
*

*> 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!!!
*

*>
*

*> Thanks!
*

*> Michel
*

*>
*

*> 2007/3/12, Dan Bolintineanu <bolintineanu_at_cems.umn.edu>:
*

*> > 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.
*

**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 ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:46:06 CST
*