[gmx-users] About Diffusion of Solvent Molecules

vidhya sankar scvsankar_agr at yahoo.com
Thu Oct 25 16:16:10 CEST 2012

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

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