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

[Sanku M]

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.

Sanku-- 
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Re: [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

--


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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