From: Peter Freddolino (
Date: Mon Sep 20 2010 - 20:34:08 CDT

Hi Sibel,
The concentration is whatever you want it to be. The only catch is that
you have to have a concentration high enough to actually allow enough
atoms to be placed to neutralize the system. If you want to have a
minimal number of ions you should just set the number ofeach type manually.

On 09/19/2010 05:37 PM, Sibel Cakan wrote:
> Dear all
> I'm interested in working with a system which include
> protein,lipid,water and ion, using the coarse grained model.
> Previously, I built a CG protein model, using the VMD CG Builder.
> Later, I run cgsolvate.tcl for solvating the system and then
> cgionize.tcl for ionization.I know the ion concentration is 0.01 for
> fully atomistic MD,but I do not know the concentration for coarse
> grained simulation.I tried 0.01 and the total charge was not zero then
> I tried 0,1 and it worked.I would like to know that the value(0.1) is
> correct?
> Thanks for help
> Sibel