[gmx-users] OPLS-AA methanol model
auryn_valemig at libero.it
Sat Jul 26 20:10:24 CEST 2008
---------- Initial Header -----------
>From : gmx-users-bounces at gromacs.org
To : "Discussion list for GROMACS users" gmx-users at gromacs.org
Date : Fri, 25 Jul 2008 17:08:53 +0200
Subject : Re: [gmx-users] OPLS-AA methanol model
> 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
> > Valentina
> 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.
> Best Regards
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> Florian Dommert
> Computational and Theoretical Softmatter & Biophysics group
> Frankfurt Institute for Advanced Studies
> Johann-Wolfgang-Goethe University
> Ruth-Moufang-Str. 1
> 60438 Frankfurt am Main
> Phone: +49(0)69 / 798 - 47522
> Fax: +49(0)69 / 798 - 47611
> EMail: dommert at fias.uni-frankfurt.de
> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
Florian!!! the world is really so little!!!
I'm Valentina, your italian friend that you have known in Amsterdam. Thank you very much. I didn't think about looking for the parameters in GROMACS force field files.
I'm going to write to you a private mail.
More information about the gromacs.org_gmx-users