[gmx-users] About the Diffusion of Water Molecules

[vidhya sankar]

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 ?