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
tutorial.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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