[gmx-users] System has non-zero total charge: 2.570000e+00

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 13 06:43:33 CEST 2009

Itamar Kass wrote:


> Hi,
> If you have non water molecule in the box (eg protein) their charge 
> might differ from 0. SO you might add ions in order to neutralize it.

In general, that is a correct solution.  But in the case of a +2.57 net charge, 
something is certainly wrong with the species in the simulation.  This charge 
represents a non-negligible rounding error that occasionally arises, and it is 
doubtful that ions alone can solve it.


> Best,
> Itamar


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


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