回复： [gmx-users] Re: Some questions on Tabulated Dihedral Potential
r.friedman at bioc.uzh.ch
Tue Jul 21 15:29:07 CEST 2009
The numerical derivative for the Nth value y[N] is calculated as:
der = y[N+1] - y[N-1] * 0.5 * deltaX
where y is the potential deltaX is the difference between two successive
values in your input (e.g., 1 if you have a table that goes from -180 to
180 with 361 values).
I don't think you can print the number without changing the code, but
it's not difficult to calculate. You can plot your forces and -der and
see where they deviate.
hong bingbing wrote:
> Hi, Ran,
> The potential f(x) and force -f'(x) in the table are calculated by
> myself before constructing the table. The potential can be written in
> an analytical form and the force is calculated as the analytical
> negative derivative of the potential at point x. There should not be
> so large deviation betw. the value I supplied and the value calculated
> by GROMACS. Wait. Is there something wrong in my interpretation?
> What's your method to get the force? Is there a way to see the
> numerical derivative generated by GROMACS?
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