[gmx-users] partial charges leading to non-zero total charge/floating point arithmetic

[Justin Lemkul]

On 4/23/18 10:29 AM, Shayna Hilburg wrote:
> Hi all,
>
> I'm setting up a system and I am getting a non-zero total charge of
> approximately 0.0002. I have several thousand ions in a system where the
> cation is a single atom of charge +2, and then the anion is a CO3 molecule
> (C with +1.3 and O with -1.1). If I change the partial charges to be full
> charges (C with +1 and O with -1), there is no longer a non-zero total
> charge.
>
> According to the error documentation, I understand this is probably due to
> floating point arithmetic, but I do not understand fully which calculation
> might be causing it and what technique I should take to have a neutral
> system. I am running in a low dielectric medium so I think the slight net
> charge could be an issue. Any suggestions would be appreciated!

You don't have any problem. The relevant discussion is here: 
https://redmine.gromacs.org/issues/2192

You're likely seeing an issue because of the 1.3 charge, per Erik's 
comment above.

Using the latest version (or any in the 2018 series) should avoid the 
note about non-zero charge.

-Justin

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

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