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
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