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As I wrote it der is the derivative itself, so you should plot (-1)*der.<br>
Ran.<br>
<br>
hong bingbing wrote:
<blockquote cite="mid280792.44938.qm@web15302.mail.cnb.yahoo.com"
type="cite">
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<div
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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)?
<div>CH<br>
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<hr size="1"><b><span style="font-weight: bold;">发件人：</span></b> Ran
Friedman <a class="moz-txt-link-rfc2396E" href="mailto:r.friedman@bioc.uzh.ch"><r.friedman@bioc.uzh.ch></a><br>
<b><span style="font-weight: bold;">收件人：</span></b> Discussion list
for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<b><span style="font-weight: bold;">已发送：</span></b> 2009/7/21(周二),
上午9:41:42<br>
<b><span style="font-weight: bold;">主题：</span></b> Re: 回复：
[gmx-users] Re: Some questions on Tabulated Dihedral Potential<br>
</font><br>
Ran Friedman wrote:
<blockquote type="cite"> Hi,<br>
<br>
The numerical derivative for the Nth value y[N] is calculated as:<br>
der = y[N+1] - y[N-1] * 0.5 * deltaX<br>
</blockquote>
Correction:<br>
der =聽 (y[N+1] - y[N-1]) * 0.5 * deltaX
<blockquote type="cite">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).<br>
<br>
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. <br>
<br>
Ran.<br>
<br>
hong bingbing wrote:
<blockquote type="cite">
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style="font-family: garamond,'new york',times,serif; font-size: 12pt;">
<div>Hi, Ran,</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Thanks</div>
<div>CH</div>
</div>
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<pre class="moz-signature">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
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<pre class="moz-signature" cols="72">--
------------------------------------------------------
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: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
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