[gmx-users] Error note

[Justin A. Lemkul]

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

-- 
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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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