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

Itamar Kass itamar.kass at gmail.com
Sun Sep 13 06:40:37 CEST 2009

Justin A. Lemkul wrote:
> najwa drici wrote:
>> hello Gromacs users,
>> I have some problems about the total charge of system using Gromacs.
>> I wanted to perform molecular dynamic simulation in box of SPC water.  
>> before energy minimization step , I performed the preprosessing step 
>> using grompp  . However, there’s a note that : System has non-zero 
>> total charge: 2.570000e+00 “.
>> why the total charge of system is not an integer?
> Something is broken.  Check the topology to see what is causing the 
> non-integral charge.  If you want any other help, you'll have to 
> describe what you're doing in much greater detail.
> -Justin
>> thank you
>> nejoua DRICI
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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.


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