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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Received on Tue Oct 04 2011 - 07:00:05 PDT
