[gmx-users] About Packing of Lipids
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?
More information about the gromacs.org_gmx-users