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 -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933536.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
