[gmx-users] About Packing of Lipids

[vidhya sankar]

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?