not sure what are looking at exactly but..
the harmonc potential used to 'pull' is k*(x-x_eq)^2
it is possible that it is k/2 instead, but that is easy to check.
Anyways, the force is -2k*(x-x_x0)= -dV/dx
so, if you look is hte output file for x_0 (where the center of the
harmonic potential should be, and x, where it is, compute the force as
described above.
So, what is it that you cannot reproduce ?
a.
On 8/31/11 7:04 PM, Sai Kumar Ramadugu wrote:
> Dear All,
> How is the force calculated during the simulated molecular dynamics?
> I'm running SMD in conjunction with Jarzynski relationship.
> The dist_vs_t file gives four columns. I was trying to the equation given by
> Klaus Schulten's PNAS article referred in AMBER 11 manual to calculate the
> force. But I cannot reproduce the force column using
> x0(t) and x and v=0.04 angstrom/ps and time step 0.002 ps.
> Any suggestions will be helpful.
>
> Thanks and regards
> Sai
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>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Wed Aug 31 2011 - 16:30:03 PDT
