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,
> > _______________________________________________
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Tue Oct 04 2011 - 08:00:03 PDT
