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Hi,<br>
<br>
Johannes Kamp wrote:
<blockquote cite="mid4A65A725.3060108@rwth-aachen.de" type="cite">
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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
cite="mid:20090720161853.12C0F246CA@struktbio205.bmc.uu.se" 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>
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