Hi Justin, I followed your comments and now at the stage of adding solvents. I wonder to see the protein after shrinking step to have no SOL molecules as there were SOL molecules in the source popc128b.pdb. Had we removed all the original SOL molecules anywhere during the course of tutorial?
I also see one of the POPC molecules standing out (upside down) of the bilayer area. How would that be adjusted? http://gromacs.5086.n6.nabble.com/file/n4999393/POPC..jpg Thanks Peterson -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999393.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 * Only plain text messages are allowed! * 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
