[gmx-users] query on partial charge entry in topology

Justin A. Lemkul jalemkul at vt.edu
Sun Nov 20 21:03:30 CET 2011

Sanku M wrote:
> Hi,
>   I find that in the ffnonbonded.itp under OPLS forcefield ( inside 
> opls.ff directory), for each particle-type, there is a partial charge 
> assigned to it. However, again in the .rtp file, for each residue, under 
> each charge group, each of the atom is assigned 
> another partial charge assigned to it. I wonder what are the purposes of 
> having two partial charge entries and which charge is actually being 
> used in simulation . My guess is that , the charge distribution assigned 
> in the .rtp file is most probably the one being used during simulation. 
> If so, then what is the purpose of having another partial charge entry 
> in the ffnonbonded.itp.
> If someone can clarify the doubt, that will be great.

It is a relic of previous development in which charges could be generalized. 
The ones in the .rtp entries are used.  Everything else is irrelevant.



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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