Dr Roitberg,
Sorry for mistake that I was missing the factor of 2.
Regards
Sai
On Wed, Aug 31, 2011 at 6:09 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> 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 - 20:30:02 PDT
