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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