[gmx-users] OPLS question
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 26 09:30:07 CEST 2004
On Wed, 2004-05-26 at 00:35, Jee E Rim wrote:
> I'm trying to put together a topology for a nicotine analogue molecule
> using the OPLS forcefield.
> Most of the atom types that I need and the force field parameters are
> already in the OPLS force field, except for a couple of dihedrals. So,
> I ran a series of single point calculations using Gaussian98 to get
> the energies of the configuration with the dihedral angles changing
> from 0 to 360, and am attempting to get the dihedral coefficients by a
> least-squares fitting to the Ryckaert-Bellemans potential function. Is
> this a good way to get the dihedral parameters? I'm using the
> optimized geometry I get from Gaussian, and am just changing the
> dihedral angles.
> The second question is, in the manual it's stated that, with the RB
> potential, the 1-4 interactions must be excluded, is this also the
> case when you're using the OPLS force field? And should I also exclude
> the 1-4 interactions when I'm using the parameters derived as above?
No! You need scaled 1/4 interactions, i.e. the vanderwaals term is
scaled by 0.5 while the coulomb term is not scaled. That you have to
take into account when deriving the dihedral terms.
> Thanks for your help in advance!
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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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