On Fri, Apr 27, 2012 at 6:31 PM, Bala S <think_bey...@aol.com> wrote:
> Justin, > > OOPS!! > Sorry for that.. Now I could realize it. > Following up.. I have done further iterations with inflategro and reached > 0.62 nm^2 which similar to what you have explained in the tutorial. > > Now, I could see the lipid bilayer really shrinked and no SOL molecules are > seen in between. Now the issue I would like to have clarification on is > that > only 163 SOL molecules were added up and down which looks very scarce for > the simulation. > > What is the solution? > > First visualize and see whether the hydrophilic ends of the lipid bilayer and your protein's part on either side of the bilayer (like a GPCR's intra and extra cellular ends) are well immersed in the water box. If not, you can increase the solvation box along the z-axis by increasing the z value for -box option in editconf (keeping x and y values same). Anirban > Bala S > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854.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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