[gmx-users] About Diffusion of Solvent Molecules
jalemkul at vt.edu
Thu Oct 25 16:26:16 CEST 2012
On 10/25/12 10:16 AM, vidhya sankar wrote:
> 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 .
You should never use such a radius for carbon. You will have huge voids in your
system that will become unstable. If a smaller value of carbon radius (on the
order of 0.375 nm) is still putting water molecules in bad locations (i.e.
within the bilayer), then your lipids are not sufficiently packed or
equilibrated. If you find yourself using extreme measures just to construct the
system, it's probably wrong.
> 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.
I don't have a clear picture of what you're describing, but it certainly sounds
wrong if my imagination is correct.
> What I mean
> Should it (Water Molcules) Be Nearer to face of the Box Throughout Entire MD . or Need not be like That?
You should have layers of solvent on either face of the membrane-protein
complex. The box should be filled (with no voids) and there should be no
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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