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

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 7:00 PM, Bala S <think_beyond at aol.com> wrote:

> Anirban,
>
> Thank you. You guys are doing miracles with the biomolecules and solving
> almost all of my problems.
>
> I have followed your suggestion and could see now some more SOL molecules
> by
> increasing the z value.
>
> But I am seeing a substantial gap between the surface of the lipid bilayer
> and added SOL molecules in the visualizer. Is it normal or I have to do
> something about it?
>
>
I didn't really get your point. From the surface means on either side of
the leaflets? Or one thing you can do is to carry out the EM, and
equilibration runs (NVT and NPT) (restraining the protein) and see how the
waters orient them with respect to the bilayer.

Anirban


> Thanks
> Bala S
>
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