[gmx-users] About Diffusion of Solvent Molecules

Justin Lemkul 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 
obvious asymmetry.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list