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

[Justin A. Lemkul]

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

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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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