[gmx-users] pairs in OPLS
spoel at xray.bmc.uu.se
Thu May 13 23:34:11 CEST 2004
On Thu, 2004-05-13 at 18:41, Lars Schaefer wrote:
> Hi all,
> I've just a simple question concerning OPLS topology: If I have defined
> a Ryckaert-Bellemans dihedral angle between, say, atoms 1-2-3-4, do I
> have to add the atoms 1 and 4 also to the [ pairs ] list nevertheless?
> The manual says:
> "If you want to include Ryckaert-Bellemans type
> dihedrals in a topology, do the following (in case of e.g. decane):
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> 1 2 3 4 3
> 2 3 4 5 3
> and do not forget to erase the 1-4 interaction in [ pairs ]!! "
> So I think I do NOT have to add my atoms 1 and 4 to the [ pairs ] list.
> But pdb2gmx does it...
> Does the manual in this respect perhaps refer to e.g. the GROMOS force
> fields only?
This is a force field question. The original Ryckaert Bellemans
potential is for carbon tails only (e.g. decane, or lipids). The same
potential is used in OPLS but with different parameters in which the
(scaled) pair interaction is part of the parameterization.
The manual does indeed need to be updated.
> Thanks in advance, Lars
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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