[gmx-users] Blowing up
farideh.khamseh at gmail.com
Sun Aug 9 09:16:59 CEST 2015
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
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?
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