[gmx-users] About Presence of Water in Hydrophobic core of lipids in NPT equlibration

Justin Lemkul jalemkul at vt.edu
Mon Nov 12 15:35:16 CET 2012

On 11/12/12 6:35 AM, vidhya sankar wrote:
> Dear Justin,
>                      Thank you for your previous reply,
>                                                                             I am  doing Protein-Lipid simulation. After Em When I visualize the str in .vmd  The water Molecules Present in Lipid (DPPC) Head groups .There is No Water Molecules Present in the Hydrophobic Part of Bilayer . While The Protein Is in the Center of box .
> Then I Have done NVT Equilibration   When I visualize the  .gro file in vmd  Around 40 Water molecules (out of 2699 )  are present in Hydrophobic part of Lipid (that is Moving inside the box, Nearer to protein which is at the center)  How to Avoid this ?

Some water will diffuse into the lipid headgroup and ester regions, which are 
largely devoid of water based on the method of increasing the van der Waals 
radius of carbon, but will normally be hydrated.  If the water molecules are 
diffusing all the way into the membrane, making contact with the lipid tails 
themselves, this would be very odd and I suspect a result of incorrect packing 
of the lipids.  That's a blind guess, and I'm not going to try to predict what's 
going on in your system, but it would be very odd for a properly equilibrated 
membrane to allow that many water molecules to diffuse deeply within it.

> May I simply delete these 40 water  Molecules  ?  or


> May I freeze these molecules During NVT Equilibration) ?

The better approach would be a position restrain along the z-axis only, allowing 
the lipids to perhaps re-orient and pack a bit better, followed by NVT 
equilibration in the absence of any restraints on water.

> Can i Leave it as such and Then Proceed Further NPT?

You could, but expect your equilibration to last significantly longer than 
normal for the hydrophobic effect to expel any water molecules that are in bad 



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


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