[gmx-users] Error note

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 23 14:26:57 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list