[gmx-users] how to define charge group?

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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