Dear Justin , Thank you For your reply I am following your Protein lipids Tutorial . I have Reached APL 61.14 A^2 Then I did Em And NVT equilibration . As stated in your Tutorial . But After NVT Equilibration When I visualize My .gro File in VMD I have Observed approximately 20 water Molecules Nearer to Protein which is in the center of box
I Think This is due to presence of some Hydrophilic Nature (Polar Nature) of Amino acids in my protein ? Is Such a diffusion of water from Hydrophilic Head Part towards polar residues of protein is Possible ? Otherwise this Behavior is odd ? May I continue NPT ? or Should I restrain the water in Z-Dimension During NVT? -- 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
