[gmx-users] non-zero total charge

[Justin Lemkul]

On 11/29/18 1:13 PM, Ali Khodayari wrote:
> Dear gmx community,
>
>   
>
> I am getting a note before performing the energy minimization step, from
> grompp that "System has non-zero charge: -0.001135". The system is a

That net charge looks somewhat large to simply be due to rounding error, 
so check your topology for errors.

-Justin

> crystalline cellulose, built in Amber, using GLYCAM06 force field and the
> topology and coordinate files have been converted to gromacs format using
> acpype. The system has zero charges with/without solvation. How important is
> this note? Is this a large value or I can just neglect it and continue with
> NVT?
>
> Thank you for your kind replies.
>
> Best
>
> Ali
>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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