[gmx-users] very small nonzero charge

[Mark Abraham]

Hi,

1. No. 2. From the look of
https://github.com/gromacs/gromacs/blob/master/src/gromacs/gmxpreprocess/nm2type.cpp#L91,
you could supply as many as fits in a double-precision value (maybe about
15), but whether the subsequent calculations retain the precision is
unclear without a detailed look at the code. I suggest you construct a toy
case with three particles whose charge is 0.333333333333333 and one of them
has a last digit of 4 and see how you go.

Mark

On Thu, Sep 27, 2018 at 11:40 AM Alex <nedomacho at gmail.com> wrote:

> Hm, i thought it was a question someone could answer...
>
>
> On Sat, Sep 22, 2018, 10:52 PM Alex <nedomacho at gmail.com> wrote:
>
> > 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?
> >
> > Thanks,
> >
> > Alex
> >
> >
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