# 回复： 回复： [gmx-users] Re: Some questions on Tabulated Dihedral Potential

hong bingbing cynthiahong1983 at yahoo.com.cn
Tue Jul 21 16:01:02 CEST 2009

```Thanks Ran. Should there also be a minus sign before (y[N+1]-y[N-1]) because the third column in the table is -f'(x)?
CH

________________________________

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 =聽 (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

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. +41-44-6355559
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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