[gmx-users] About Packing of Lipids

Justin Lemkul jalemkul at vt.edu
Sat Dec 1 14:19:11 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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