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:
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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