[gmx-users] OPLS-AA Coulomb-14 energies incorrect?
lindahl at stanford.edu
Wed Aug 6 09:26:01 CEST 2003
It's always nice to see comparisons!
First - I think I know what the cause of the difference might be. By
default, the pdb2gmx program does not generate 1,4 interactions for
hydrogens since that's the prescribed setup for the other force fields.
Use the -H14 flag for pdb2gmx to get the OPLS-AA standard.
This will probably be the default in future Gromacs versions (it's
already changed in CVS), but we would probably confuse users more by
changing the default in a point release....
The parameters have mainly been cross-validated with Tinker, the
energies for aminoacids in the Jorgensen publications (check the header
of the force field for references) and MacroModel.
> The Coulomb (SR) component of the GROMACS energy agrees with the
> corresponding energy from TINKER (i.e. as calculated by setting
> chg-14-scale to 0.0), but the Coulomb-14 energy is out by a sizeable
> percentage. i.e for the attached file GROMACS reports 224.739 kJ/mol
> while TINKER reports 258.3687 kJ/mol.
Again, I would guess that difference is due to not using the -H14 flag.
You are right that the relative difference for this term is large, but
compared to the total nonbonded energy it is very small, so it is not
likely to have affected your simulations significantly.
> Comparing GROMACS (OPLS-AA parameter files checked out of CVS about
> a month ago) and TINKER 4.0 (with the supplied oplsaa.prm parameters)
> a couple of potential energy calculations, I found that they agree on
> the bond stretch, bend and LJ energies. The improper dihedral energies
> differ, though this may be due to a problem with TINKER. GROMACS uses
> some updated proper dihedral parameters, absent from the TINKER.
Right - the bonded parameters are essentially the Amber ones, and they
haven't been changed in years. There are two major modifications to the
OPLS torsion angles not present in Tinker (one by Jorgensen in 1999 and
another set that formed the OPLS-AA/L version in 2001). I also recall
there were some minor issues in Tinker; some uncommon charge groups
would not end up being neutral with their charges.
Another issue you might stumble upon is that Amber and Gromacs used
different atom orders for the improper dihedrals. I've changed this in
our later versions, but this is not significant. The difference is only
second order, and the improper force constants are just
order-of-magnitude guesses anyway. I've just uploaded a tarball with
the latest OPLS parameters to the contrib section of www.gromacs.org if
you want to play with it.
In all cases of doubt I've used the "original" values, i.e. Amber for
bonded interactions and Jorgensen/Kaminski for torsions and charges. I
also communicated rather extensively with Bill Jorgensen and Julian
Tirado-Rives during the implementation (they were quite helpful).
Thanks for the help with checking things - and let me know if the
problems persist with -H14.
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