[gmx-users] Dismantling the methyl group

Jussi Lehtola jussi.lehtola at helsinki.fi
Mon Jul 2 12:27:12 CEST 2007


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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