[gmx-users] About pritein Lipid Bilayer Simulation

Justin Lemkul jalemkul at vt.edu
Sat Oct 6 11:54:43 CEST 2012

On 10/6/12 1:35 AM, vidhya sankar wrote:
> Dear Justin , Thank you for your Previous reply
>                           using Genbox I have  Successfully Solvated  Energy Minimized  "System_shrink.gro" file  It adds 84266 water molecules .  Then  Tutorial How to Check Existence of Water Molecules within HydroPhobic  core of Bilayer  it is  Difficult to  see and detect in VMD

Solvation should only be done at the very end, after a few dozen rounds of 
shrinking.  Are you working through the tutorial or a system of your own?  If 
you're doing the tutorial, the amount of water molecules is far too high.  Water 
molecules within the hydrophobic core of the membrane should be obvious upon 
visualization (there should only be a few, at most, if the system is constructed 
properly).  Methods for dealing with these stray molecules are described in the 



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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