Dear Justin, Thank you for your Previous reply. I am Extending your Protein Lipid tutorial To my System I am using DPPC128.pdb Which Surround the Cyclic Peptide. As You Quoted in tutorial I am Solvating My Lipid-protein Environment Using 148 Molecules (By genbox tools while
I am using Vanderwalls Radii 0.92 for Carbon atom ) When I visualize .gro File in VMD Most of the water Molecules Are near the Face of My box ( Away from center) while Lipid molecules are concentrated Around Protein Which is at The center of box . After Second Phase Equilibration (After NPT ,Same Parameter ) When I see .gro file in VMD Most of Water Molecules moved inside the box ( Surround the Protein along with the Lipid molecules ) Is this Type of Diffusion of Solvent molecules is Usual or Not. What I mean Should it (Water Molcules) Be Nearer to face of the Box Throughout Entire MD . or Need not be like That? Thanks In Advance -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
