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