[gmx-users] OPLS-AA methanol model
dommert at fias.uni-frankfurt.de
Fri Jul 25 17:08:53 CEST 2008
On Jul 25, 2008, at 2:32 PM, auryn_valemig wrote:
> Hi to everybody!!!
> I have some problem in understanding which geometry of methanol is
> used by the OPLS- all atom force field (JACS, 1996, 118, 11225). Do
> you know if it is the experimental geometry (determined by Lees and
> Baker- j. chem phys. 1968, 48, 5299)? In the paper published on JACS
> in 1996 there are no details on the geometries of the models they
> are parametrizing.
> Moreover, do you know if I can find somewhere the topology file for
> this methanol model (from the download topologies page I've
> downloaded the topology but there are no geometric parameters-
> distances, angles and diedrals.)
> Thank you in advance
I do not know the papers you mentioning, however if there is a
paramerization of an molecule in OPLS-AA parameters you also have the
geometry. The equilibrium bond lengths and angles are given
explicitly, I think, because they are OPLS-AA parameters. For the equ.
dihedral angles, just plot the Fourier Series and you will see the
dihdrals at the corresponding minima of the function. This should
allow you to build up a molecule corresponding to the Force Field.
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