[gmx-users] Re: Why does x2top need to clean dihedrals?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Fri Oct 9 09:23:30 CEST 2009

>x2top -h

>Did you use the -alldih flag? For OPLS like force field all dihedrals
are need, for gromos like ff only one dihedral per bond is kept, that is


Thanks, David. I did not use -alldih. After I used it, four dihedrals
for one bond are all kept. Anyway I have got this point about the
difference of defining dihedral between OPLS and Gromos ff, though I
still don't clearly understand why difference exists.


>David van der Spoel, Ph.D., Professor of Biology

>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala

>Box 596, 75124 Uppsala, Sweden. Phone:         +46184714205. Fax:

>spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se



Zhongqiao Hu

Dept of Chem & Biomol Engineer

National Univ of Singapore


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