Dear Justin Thank you for your Previous reply,
I am following your Protein -Lipid tutorial . I am doing simulation of Assembly of Cyclic Peptide ( Made up of Only Phenyl alanine Residue) in DPPC lipid . After I have Attained suitable APL (69 A^2) I solvated, neutralized (using genion) & EMzed . Finally I Have Done NVT equilibration Using Restraint on all atoms of Lipid Molecules . At the End of My simulation I Have observed some of water molecules (60 water Molecules ) in Hydrophobic Part of Lipid Molecules (Amidst of Assembly of cyclic peptide) How to Avoid this ? Should Further Shrink APL using Perl And Then Proceeding NVT Equilibration ? -- 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
