On 10/11/2011 12:52 AM, Thomas Schlesier wrote:
Hi all,
for a publication i want to list the used OPLS parameters for the
investigated molecules. In GROMACS all atomtypes are uniquely defined
by the atomtype `opls_xyz`. And from the atomtypes one can deduct the
bonded parameters. So it is sufficient to list only the atomtypes and
probably charges.
My question is now, is this definition common knowledge, or only
GROMACS-intern? From the header of `ffoplsaa.atp` one sees that the
first 65 atomtypes are for the OPLS-UA force field, and the names of
the atomtypes are the same as in the paper which is mentioned.
Concerning the OPLS-AA force field, is there the GROMACS numbering
scheme also common knowledge?
If you consult the paper in which OPLS-AA was published (which you no
doubt read before simulating with OPLS-AA), you will see that the
numbering scheme is not internal to GROMACS.
Mark
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