Gavin Melaugh wrote:
I am using 4.5.5
The warning is only triggered if the charge group is 10 atoms or larger. Why
this is the threshold, I can't say. I didn't write the code ;)
You may still want to do some tests with smaller charge groups to make sure the
changes do not produce significantly different energies.
-Justin
Justin A. Lemkul wrote:
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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