[gmx-users] About Presence of Water in Hydrophobic core of lipids in NPT equlibration
scvsankar_agr at yahoo.com
Mon Nov 12 12:35:35 CET 2012
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
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