[gmx-users] Some questions on Tabulated Dihedral Potential
hong bingbing
cynthiahong1983 at yahoo.com.cn
Mon Jul 20 17:49:18 CEST 2009
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?
There're also some other confusions:
1. Can the constant k before the cubic spline function be defined arbitrarily, as long as the multiplication of k and f(x) equals to the dihedral potential?
2. The tables do not need to be supplied to mdrun using '-tableb', right? I found if I omitted -tableb and the following table files, GROMACS can still go and find the two tables.
3. how to use '-tableb' if two tables are supplied? '-tableb table_d1.xvg table_d2.xvg' or '-tableb table_d1.xvg -tableb table_d2.xvg'? I tried both and error information was given that GROMACS can not find 'table_d1_d1.xvg'. I then delete '_d1' in both of the commands and there was no error information any more. It seems that only one table can be supplied to mdrun by using'-tableb', the second table can not be recognized all the time.
Thanks for your help
CH
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