[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Bala S think_beyond at aol.com
Fri Apr 27 12:40:55 CEST 2012

Thanks for the reply.

I'm following the tutorial.

In your system, to solvate it you have the values that was used during the
protien insertion into the bilayer. Following it, I have used the following
commandfor my system where the protein is very much smaller than the length
of the bilayer.

$ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 6.59650

$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top

But I could see in the visualizer that SOL molecules were added on top and
bottom but only 1/3 of the length of the bilayer. 
How to add SOL molecules to whole length or how to remove not-solvated part
of lipids?

Bala S

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