[gmx-users] Re: Some questions on Tabulated Dihedral Potential
Ran Friedman
r.friedman at bioc.uzh.ch
Tue Jul 21 14:17:11 CEST 2009
Hi,
Johannes Kamp wrote:
> Hi Cynthia,
>
> 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.
>
>> Dear all,
>>
>> 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:
>>
>> 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
>> 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
>>
>> 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?
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.
Good luck,
Ran
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