[gmx-users] very small nonzero charge

Alex nedomacho at gmail.com
Sun Sep 23 06:52:51 CEST 2018

Hi all,

I am dealing with a solid structure with partial charges initially 
obtained from DFT and adjusted to work with MD. It just so happens that 
the total charge of the system, however small, will always be nonzero. 
The reason is trivial and unfortunately unavoidable, given the 
geometries. It sounds silly, but this is the situation. It has to do 
with division by three and one of the partial charges will have to have 
the form of e.g. 0.333333... Hence, a few questions:

1. Is the total charge of the system of the order ~1e-6 expected to 
produce artifacts with the latest versions of GMX (we're using 2018.1)?

2. The total charge will go down with the number of digits readable by 
x2top from atomname2type, so what's the max number of digits I could supply?



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