[gmx-users] About Packing of Lipids

[Justin Lemkul]

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

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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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