[gmx-users] how to define charge group?

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 27 00:32:56 CEST 2011

Sanku M wrote:
> Hi,
>   I am trying to write a topology in gromacs format for a recently 
> developed molecule in OPLS format. From the parameterization-paper, I 
> know the partial charges on each of the atom in that molecule from the 
> corresponding paper . But, I am not sure how to split the molecule 
> topology into several charge-groups. I mean, is there any thumb-rule on 
> how to define opls charge groups for using in gromacs. Only thing I know 
> from mailing list is that one should not use large charge-groups. But, I 
> was wondering if someone can provide some input on how to define 
> charge-groups.
> Sanku

Please read section 3.4.2 in the manual, particularly the "Charge groups" 
section.  Charge groups need not have integral charge if using PME.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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