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

[Ran Friedman]

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