(no subject)

From: Boshra Moradi (boshra.moradi.1983_at_gmail.com)
Date: Tue May 06 2014 - 16:35:44 CDT

I put a rigid (fix) protein in a water box with 6000 water molecules and
run NAMD. I had 250 steps for dcd. I chose the water molecules around
protein with distance of 3 A. Now I want to survey the interactions
between atoms of the protein and water molecules with quantum method but I
have a problem and it is: I should have one arrangement of water molecules
around the protein and I don't know how can I choose the best equilibrium
arrangment of water molecules ( in view point of energy) between these 250
 I will appreciate very much if
anyone can give me any advice.
Thanks in advance

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