[gmx-users] Non-zero total charge

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 1 15:09:44 CEST 2011

Munishika Kalia wrote:
> Hi,
> My system had a no zero total charge:
> System has non-zero total charge: 6.300000e+01
> I used genion to neutralize the system by adding 6 CL ions.
> After updating the topology file, the system still seems to have the 
> same problem.
> It still has a non-zero total charge:
> System has non-zero total charge: 5.700000e+01
> Please let me how i can rectify the situation.

You haven't provided your genion command line (for the future, please always 
provide the exact command you used), but I suspect I know what the problem is 
anyway.  You added 6 CL- ions, right?  You initially had a +63 charge (6.3e+1 = 
6.3 x 10^1).  Hence you still have an unsatisfied charge of +57.



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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