[gmx-users] non-zero total charge

Discussion:

Ali Khodayari

2018-11-29 18:13:56 UTC

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
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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Dallas Warren

2018-11-30 00:52:24 UTC

Permalink

http://www.gromacs.org/Documentation/Errors?highlight=periodicity#System_has_non-zero_total_charge

On Fri, 30 Nov. 2018, 5:14 am Ali Khodayari <

Post by Ali Khodayari
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
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 Lemkul

2018-11-30 19:28:24 UTC

Permalink

Post by Ali Khodayari
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

Post by Ali Khodayari
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

Ali Khodayari

2018-11-30 21:06:01 UTC

Permalink

Dear Justin,
Thank you for your reply.
I've checked it several time, and "to me" it looks fine. What exactly should
be checked. Anything in particular?
Best,
Ali

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

Post by Ali Khodayari
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

Post by Ali Khodayari
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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

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

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Ali Khodayari

2018-11-30 22:07:00 UTC

Permalink

Solved!
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
beginning!
Kind regards,
Ali

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

Post by Ali Khodayari
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

Post by Ali Khodayari
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