[gmx-users] About Packing of Lipids
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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