VMD-L Mailing List

From: Sibel Cakan (sibelc_at_stu.khas.edu.tr)
Date: Sun Sep 19 2010 - 16:37:15 CDT

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