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

[vidhya sankar]

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 ? 

May I simply delete these 40 water  Molecules  ?  or
May I freeze these molecules During NVT Equilibration) ?
Can i Leave it as such and Then Proceed Further NPT?

I Hope Your Valuable Suggestion?


Thanks in Advance