[gmx-users] OPLS-AA methanol model

[auryn_valemig]

---------- Initial Header -----------

>From      : gmx-users-bounces at gromacs.org
To          : "Discussion list for GROMACS users" gmx-users at gromacs.org
Cc          : 
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
> >
> 
> Hello,
> 
>   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
> 
> Flo
> 
> 
> >
> >
> > _______________________________________________
> > 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
> Dipl.-Phys.
> 
> 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.
Bye Bye

Vale