[gmx-users] partial charge and LJ parameters for CH3 in gromos forcefields

Justin Lemkul jalemkul at vt.edu
Thu Feb 20 04:24:13 CET 2014

On 2/19/14, 1:00 PM, leila salimi wrote:
> Dear users,
> I have CH3 in my molecule and in gromos force filed partial charges for CH3
> is 0 (as the united atom of the GROMOS forcefield) and It doesn't consider
> single H atoms,  but "includes" these H atoms into the C atoms. That means
> that the CH3 group is just one LJ-bead in the GROMOS forcefield.
> I need to know the charge for C and H separately, Do you know any solution
> for that?
> I wnat to use CP2K and as I understand correctly in CP2K I have to define
> charges and LJ parameters for each atoms.
> Is there any  program available to convert gromacs file to other format,
> like CHARM format?

Under the GROMOS force fields, CH3 is an "atom."  It's just a united-atom.  I 
don't know what good these parameters would do in CHARMM format, but if you want 
to use a CHARMM all-atom topology instead, there is no conversion necessary (or 
possible), just use the CHARMM force fields.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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