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

Ran Friedman r.friedman at bioc.uzh.ch
Tue Jul 21 16:09:20 CEST 2009

```As I wrote it der is the derivative itself, so you should plot (-1)*der.
Ran.

hong bingbing wrote:
> 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
>
>
>
>
>
> ------------------------------------------------------------------------
> *发件人：* Ran Friedman <r.friedman at bioc.uzh.ch>
> *收件人：* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *已发送：* 2009/7/21(周二), 上午9:41:42
> *主题：* Re: 回复： [gmx-users] Re: Some questions on Tabulated
> Dihedral Potential
>
> 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 聽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
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> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
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> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355559
> Email: r.friedman at bioc.unizh.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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