[gmx-users] OPLS-AA methanol model

[Florian Dommert]

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


>
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--
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

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