[gmx-users] charge group number

[Justin Lemkul]

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)
> as
> follows:
>
> 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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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