On Fri, Apr 27, 2012 at 7:00 PM, Bala S <think_bey...@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 > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933923.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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