[gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution

[Justin Lemkul]

On 4/16/20 10:26 AM, Adarsh V. K. wrote:
> Dear all,
>
> While performing a protein ligand simulation, I received the following
> 'WARNING' message. How to manage this issue? just with ' -maxwarn 1 ' or
> any other method?
>
> -------------------------------------------------------------------------------------------------------
> gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o
> nvt.tpr
>
> WARNING 1 [file topol.top, line 60334]:
>    You are using Ewald electrostatics in a system with net charge. This can
>    lead to severe artifacts, such as ions moving into regions with low
>    dielectric, due to the uniform background charge. We suggest to
>    neutralize your system with counter ions, possibly in combination with a
>    physiological salt concentration.
> -------------------------------------------------------------------------------------------------------

The warning suggests what you should do. Your system isn't neutral but 
with PME it should be to avoid potential artifacts.

Don't use -maxwarn to override cases in which grompp tells you that 
you're doing something unphysical.

-Justin

-- 
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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

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

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