[gmx-users] non-zero total charge

Ali Khodayari ali.khodayari at student.kuleuven.be
Fri Nov 30 23:07:09 CET 2018

I checked the topology. However, a qtot of 0.000 was shown at the end of
atoms section, yet, 1152 atoms had an extra plus/minus 0.000001 charge which
added up to 0.001135 extra net charge. Rounding these numbers to zero
removed the note, leading to a zero total charge.
Nevertheless, I don't have any idea from where they were generated in the
Kind regards,

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin
Sent: vrijdag 30 november 2018 20:28
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] non-zero total charge

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.


> 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


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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