On Fri, Apr 27, 2012 at 3:27 PM, Bala S <think_bey...@aol.com> wrote:
> Thank you for that clarification. > > I found that there were SOL molecules in .top file. I could run the EM now. > > Coming to the Solvation step, I'm facing a problem. > > I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat > locally. > > While adding the solvent molecules, what command should I be using? > > I am using the usual command I use for non-membrane simulations, > > $ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic > > followed by > > $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top > When you mention -bt cubic, it adds a cubic water box all around your system (if you visualize you will see your entire bilayer immersed in a cubic water box like a normal protein solvation). But that is wrong. You need to add water only on either side of the lipid membrane (that is along the z-axis only). So use the -box option with editconf without using -c and -d. You can have a look at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly mentioned over there how to go about it. > > calculation goes for long time showing a huge number of SOL molecules. > > I guess I'm worng somehere. > > Thanks. > > Bala S > > > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.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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