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

[Bala S]

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?

Thanks
Bala S

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