[gmx-users] Solvating a CG system

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 30 13:28:31 CET 2009

Anirban Ghosh wrote:
> Hi ALL,
> I have a CG protein in a CG lipid bilayer. I have packed the lipids 
> around the protein using InflateGRO, following Justin's tutorial. Now I 
> want to solvate it with CG waters. In all-atom we need to set a higher 
> value for VanderWaal's radii for C in vdwradii.dat file. What should it 
> be like for solvating my CG system, since there are no "C" here? Is 
> there any different file for that? I tried using genbox normally and 
> fornd CG waters inserted between the CG protein beads. How to solve this?
> Any suggestion is welcome.

Add entries in vdwradii.dat for the atom types in your CG model, or remove the 
stray particles manually or with a script like those found here:



> Regards,
> Anirban
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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