Hi Jussi,
Gromacs only handles the methyl as a single particle if you tell it
to, i.e. by taking a united atom force field like GROMOS. You can use
OPLS/Amber in stead. Of course you can add the hydrogens based on an
ideal geometry for each frame, but I think you'll miss part of the
points of generating structures for electronic calculations in that
case.
Cheers,
Tsjerk
On 7/2/07, Jussi Lehtola <[EMAIL PROTECTED]> wrote:
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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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