<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div 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 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><br></div><div><br></div><div style="font-family:garamond, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font size="2"
face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">发件人：</span></b> Ran Friedman <r.friedman@bioc.uzh.ch><br><b><span style="font-weight: bold;">收件人：</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">已发送：</span></b> 2009/7/21(周二), 上午8:17:11<br><b><span style="font-weight: bold;">主题：</span></b> Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential<br></font><br>
Hi,<br>
<br>
Johannes Kamp wrote:
<blockquote type="cite">
Hi Cynthia,<br>
<br>
I'm also working on including some tabulated functions but I don't have
any simulation yet. Thus I'm not a 'specialist' in this topic, but I
hope I can help you a little.<br>
<br>
<blockquote type="cite">
<div style="font-family:garamond, 'new york', times, serif;font-size:12pt;color:rgb(0, 0, 0);">Dear
all,
<div><br>
</div>
<div>I tried to include 2 tabulated dihedral potential functions
into
my simulation. But it seems to be not able to generate correct results.
The system just exploded. I defined 3601 points in each table (from
-180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two
warning information:</div>
<div><br>
</div>
<div>WARNING: For the 3598 non-zero entries for table 0 in
table_d1.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential</div>
<div>WARNING: For the 3598 non-zero entries for table 0 in
table_d2.xvg the forces deviate on average 193% from minus the
numerical derivative of the potential<br>
<div> </div>
<div>Do these two warnings matter very much? I checked the values
for
x,f(x),-f'(x) in the tables and don't think there're mistakes. has
anyone of you met with such problems? <br>
</div>
</div>
</div>
</blockquote>
</blockquote>
In the tables you should supply potentials and forces. The forces are
also calculated numerically, and a warning is emitted if the numerical
derivatives deviate too much from the forces supplied by the user.
Since the forces are interpolated, if the numerical derivative is too
far from the input what you'd get will be different then expected. You
can calculate the derivatives yourself and see where there are
deviations.<br>
<br>
Good luck,<br>
Ran<br>
</div></div><div style="position:fixed"></div></div><br>
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