[gmx-users] OPLS united atom
Krzysztof Murzyn
ubmurzyn at cyf-kr.edu.pl
Tue Jul 9 10:13:21 CEST 2002
Hi,
I'd like to transfer OPLS united atom forcefield as implemented in Amber
package (files: opls_parm.dat and aa residues definitions) into the
Gromacs format. The first problem I faced concerns dihedrals.
The Amber definitions give 1/2 of the rotation barrier magnitude (in units
kcal/mol), periodicity and the phase (0 deg if an energy MAXIMUM is at 0
deg or 180 deg if an energy MINIMUM is at 0 deg; 0 deg corresponds to
the cis conformation). This form matches (?) Gromacs definition with the
function form eq 1. Amber definitions of some dihedrals consist of a few
terms resulting from deconvolution of the full dihedral potential into a
Fourier series. Each term is given in a form described above and it
happend that terms for a single dihedral have a different phase.
My question is how I could properly transfer these parameters in the
Gromacs world. An obvious solution would be to list all terms for each
torsion with func eq 1 but this implies that one Gromacs dihedral
definition would consist of several entries/lines. Would it be OK?
Regards,
Krzysztof
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