[gmx-users] Dismantling the methyl group
erikm at xray.bmc.uu.se
Mon Jul 2 12:58:18 CEST 2007
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.
2 jul 2007 kl. 12.27 skrev Jussi Lehtola:
> I've run into problems with simulating a methanol - water system. My
> purpose is to do an electronic structure calculation for
> 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
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users