[gmx-users] About Packing of Lipids

vidhya sankar scvsankar_agr at yahoo.com
Sat Dec 1 14:17:21 CET 2012

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?

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