On Tue, Oct 4, 2011 at 3:10 PM, Ali M. Naserian-Nik
<naseriannik.gmail.com>wrote:
> 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?
>
Both are obtained from coordinate files initially (x0,y0,z0 from the refc
file, x,y,z from the coordinate file). However, after every step and
positions are updated, the x,y,z just comes from the global coordinate
array.
>
> I have to set nscm=0, therefore the center of mass of system transforms
> during simulations. How do I must act in this case?
>
I don't understand what you're asking. You should set nscm=0, since the COM
shouldn't move much (since your'e being restrained to a fixed position in
space).
HTH,
Jason
>
>
> 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,
> > > > _______________________________________________
> > > > 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
> > >
> >
> >
> >
> > --
> > 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/amber
> >
> _______________________________________________
> 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
Received on Tue Oct 04 2011 - 12:30:05 PDT
