[gmx-users] Some questions on Tabulated Dihedral Potential

[hong bingbing]

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


      ___________________________________________________________ 
  好玩贺卡等你发，邮箱贺卡全新上线！ 
http://card.mail.cn.yahoo.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090720/ec71353f/attachment.html>