[gmx-users] Dismantling the methyl group

[Erik Marklund]

Hi,

You should use an all-atom force field. I assume you're using one of  
the Gromos force fields, which is of united-atom type.

/Erik

2 jul 2007 kl. 12.27 skrev Jussi Lehtola:

> Hi,
>
>
>
> I've run into problems with simulating a methanol - water system. My
> purpose is to do an electronic structure calculation for  
> configurations
> generated with Gromacs, however the thing is that Gromacs handles the
> methyl group as a single unit whereas I need the coordinates of the
> carbon and of the three hydrogens for the quantum mechanic  
> computations.
>
> Is there any simple way to put the hydrogens in place using  
> Gromacs, or
> do I need to program a way myself?
> -- 
> Mr. Jussi Lehtola
> Research Assistant
> Division of Theoretical Physics / Division of High Energy Physics
> IT services
>
> Department of Physical Sciences
> University of Helsinki
>
>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys