[gmx-users] charge group number
jalemkul at vt.edu
Wed Mar 5 12:10:13 CET 2014
On 3/5/14, 5:25 AM, Chetan Mahajan wrote:
> Hi All
> I am just learning how to assign charge group number. For TiO2 slab,
> amber2gromacs tool (acpype) I used assigns cgnr increasing consecutively
> from Ti atoms followed by oxygen atoms. Clearly charge group here ( either
> Ti or O) does not have zero charge. Can anyone throw light on why cgnr
> should be like this (individual atoms) here?
> Also in formate anion, should I have charge groups (charge in the bracket)
> charge group 1 : C (0.9) and O (-0.88) together
> charge group 2 : O (-0.88)
> charge group 3: H (-0.147)
If you are using PME, there is no requirement that charge groups contain
integral charges. Most force fields (including AMBER!) do not use multi-atom
charge groups, so each atom in its own group is fine.
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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