[gmx-users] dihedral doubts, again
Jones de Andrade
johannesrs at gmail.com
Sat Jul 28 00:27:17 CEST 2007
Well, I'm having a few problems in implementing an opls-like dihedral
potential, what mean, a serie of different periodic dihedral potentials.
After much problem with the RB potential conversion, Ifound on the net that
the 3.3.1 version of gromacs allows me to use sum of different periodic
potential for the same dihedral, making it unecessary to use RBs. So, if I
wrote the dihedrals in the form:
F CT CT F 1 0.00 0.0000
F CT CT F 1 180.00 5.20800
X CT CT X 1 0.00 0.6530
And grompp at least "swallowed" it. But I'm not quite sure if I understand
how is he dealing with it.
>From what I understand, the first two potential will sum up together to
describe the dihedral of F-CT-CT-F. Then, all other dihedrals centered in a
bond CT-CT and that haven't been explicit defined before will be defined by
the potential described in the fourth line, correct?
If anyone could please clarify this matter better for me I would be very
Thanks a lot in advance for anything.
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