On 12/1/12 8:17 AM, vidhya sankar wrote:
Dear Justin ,
Thank you For your reply
I am following your Protein lipids Tutorial . I have Reached APL 61.14 A^2
Then I did Em And NVT equilibration . As stated in your Tutorial . But After
NVT Equilibration
When I visualize My .gro File in VMD I have Observed approximately 20 water
Molecules Nearer to Protein which is in the center of box
I Think This is due to presence of some Hydrophilic Nature (Polar Nature) of
Amino acids in my protein ?
Is Such a diffusion of water from Hydrophilic Head Part towards polar residues
of protein is Possible ? Otherwise this Behavior is odd ?
May I continue NPT ? or Should I restrain the water in Z-Dimension During NVT?
And why shouldn't polar amino acids attract water? Please apply some basic
biochemical knowledge here.
-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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