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

[hong bingbing]

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

 






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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
Postdoctoral Fellow
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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