Dear Jason and Daniel,
Thank you very much for your reply.
Please assume that an atom is restrained to its initial position through a
positional restrain with a weak force constant. Then I think Fx=k(x-x0),
Fy=k(y-y0), and Fz=k(z-z0) and the resultant force applied to the restrained
atom is F=(Fx^2+Fy^2+Fz^2)^(1/2), where (x0,y0,z0) the initial coordinate of
the atom as Jason said and (x,y,z) must be obtained from crd file. It is
true?
I have to set nscm=0, therefore the center of mass of system transforms
during simulations. How do I must act in this case?
On Tue, Oct 4, 2011 at 5:59 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> 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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> > > AMBER.ambermd.org
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> > >
> >
> >
> >
> > --
> > 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
> >
>
>
>
> --
> 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 - 12:30:03 PDT
