[gmx-users] Blowing up

[faride badalkhani]

Dear Victor,

Thanks a lot for your answer. Could you introduce me a guidance for
defining proper charge groups?

Truly yours,
Farideh


On Mon, Aug 10, 2015 at 5:44 PM, Victor Rosas Garcia <rosas.victor at gmail.com
> wrote:

> it could be, but it might just be easier to try redefining smaller charge
> groups and run the dynamics again.
>
> Hope this helps
>
> Victor
>
> 2015-08-09 2:16 GMT-05:00 faride badalkhani <farideh.khamseh at gmail.com>:
>
> > Dear all,
> >
> > I am truing to do an MD simulation on dendrimeric structures. I can
> perform
> > all steps successfully, but I get a NOTE in all steps after Adding Ions
> as
> > follows:
> >
> > NOTE 2 [file topol.top]:
> >   The largest charge group contains 20 atoms.
> >   Since atoms only see each other when the centers of geometry of the
> > charge
> >   groups they belong to are within the cut-off distance, too large charge
> >   groups can lead to serious cut-off artifacts.
> >   For efficiency and accuracy, charge group should consist of a few
> atoms.
> >   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> >
> > Finally at the production MD step I get a "X particles communicated to
> PME
> > node Y are more than a cell length out of the domain decomposition cell
> of
> > their charge group".
> >
> > Do you think is it because of the mentioned note?
> >
> > Truly yours,
> > Farideh
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