[gmx-users] Blowing up

Victor Rosas Garcia rosas.victor at gmail.com
Mon Aug 10 15:14:32 CEST 2015

it could be, but it might just be easier to try redefining smaller charge
groups and run the dynamics again.

Hope this helps


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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