Ran Friedman wrote:
Hi,
The numerical derivative for the Nth value y[N] is calculated as:
der = y[N+1] - y[N-1] * 0.5 * deltaX
Correction:
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.
Ran.
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?
Thanks
CH
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--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.unizh.ch
Skype: ran.friedman
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