[gmx-users] About Diffusion of Solvent Molecules
scvsankar_agr at yahoo.com
Thu Oct 25 16:16:10 CEST 2012
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
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