[gmx-users] Dismantling the methyl group

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 2 12:55:28 CEST 2007

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



On 7/2/07, Jussi Lehtola <jussi.lehtola at helsinki.fi> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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

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

More information about the gromacs.org_gmx-users mailing list