Gavin Melaugh wrote:
Hi Justin
I saw this and had a question.
How important is it for a charge group to be neutral?
It isn't. Conventional use dictates that the charge group bear an integral
charge. With PME, this is not necessary. Many force fields do not use charge
groups at all (i.e., single-atom charge groups).
In one of my systems I model a solvent of crown ethers using an all atom
model. The smallest neutral unit comprises a CH2-O-CH2 (7 atoms). I have
used this as a charge group to and get no warnings.
The only implication I can think of would be in neighbor searching. If the
group is large, then short-range forces may not be calculated accurately. The
warning from grompp was a recent addition to the code; if you're using an older
version you may not have triggered it.
-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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