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From: Daniel Sindhikara <sindhikara.gmail.com>

Date: Tue, 4 Oct 2011 23:29:38 +0900

I think what Ali is looking for is the force in the x direction which is

-2*k(x-x0) (for NMR restraints)

k and x0 are in your input/restraint file (and are constant).

I cant recall if x(t) is output directly to a file, you may need to use

ptraj on your trajectory to get it.

On Tue, Oct 4, 2011 at 10:51 PM, Jason Swails <jason.swails.gmail.com>wrote:

*> On Tue, Oct 4, 2011 at 3:49 AM, Ali M. Naserian-Nik
*

*> <naseriannik.gmail.com>wrote:
*

*>
*

*> > Hi all,
*

*> >
*

*> >
*

*> > Would you please explain how is it possible to calculate the force, which
*

*> > is
*

*> > applied to a point restrained by a harmonic potential? I think F =
*

*> k(x-x0)
*

*> >
*

*>
*

*> You mean (x-x0) ^ 2?
*

*>
*

*>
*

*> > formula can be used for this purpose; but then is there any way to
*

*> > obtain x0and x of the restrained point during the simulation?
*

*> >
*

*>
*

*> Are you talking about positional restraints or NMR restraints? In either
*

*> case, it's fairly straightforward. You have the form of that potential
*

*> term
*

*> (F=k(x-x0)^2) along with all atomic coordinates. You have everything you
*

*> need to take the analytic gradient of that potential term wrt. the atomic
*

*> positions, which IS the force.
*

*>
*

*> If your question is about x and x0, then the positions at every point are
*

*> known, so they're just taken from that... For positional restraints, x0
*

*> doesn't move (unless transformations are done on the whole system), but
*

*> those are read in at the beginning of the simulation. For NMR restraints,
*

*> x0 is supplied in the restraint input file. The "x" positions are just
*

*> taken from the coordinate array at every step those forces are calculated.
*

*>
*

*> HTH,
*

*> Jason
*

*>
*

*>
*

*> >
*

*> >
*

*> >
*

*> > I would be so grateful if anyone could help me on these issues.
*

*> >
*

*> > Kind regards,
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*>
*

*>
*

*>
*

*> --
*

*> Jason M. Swails
*

*> Quantum Theory Project,
*

*> University of Florida
*

*> Ph.D. Candidate
*

*> 352-392-4032
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Tue, 4 Oct 2011 23:29:38 +0900

I think what Ali is looking for is the force in the x direction which is

-2*k(x-x0) (for NMR restraints)

k and x0 are in your input/restraint file (and are constant).

I cant recall if x(t) is output directly to a file, you may need to use

ptraj on your trajectory to get it.

On Tue, Oct 4, 2011 at 10:51 PM, Jason Swails <jason.swails.gmail.com>wrote:

-- Dr. Daniel J. Sindhikara Institute for Molecular Science E-mail: sindhikara.gmail.com Website: http://sites.google.com/site/dansindhikara/ -- _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Oct 04 2011 - 08:00:03 PDT

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