keep in mind that each water molecule stands for itself and its images in all the periodic cell units.
2010-09-20
Ye MEI
From: Rilei Yu
Date: 2010-09-20 10:53:47
To: amber
CC:
Subject: [AMBER] molecular dynamics simulation-water-box-diffution problem
Dear amber users,
After simulation on my protein for 10ns, I found water molecules diffuse considerably. When I tried to analysis it in the VMD, keeping water with 5 angstrom distance from the protein, I could only find several water molecules. To solve this problem, I have checked the mail-list, and found some people suggest use iwrap=1.
But here I still have some questions:
1 Although, the water molecules diffused considerably, the dynamics property of my protein was normal.
2 In fact I adopted the md simulation parameters from the tutorial: http://ambermd.org/tutorials/basic/tutorial1/section6.htm. I found in the tutorial the water molecules also diffuse to some degree in the 120 ps MD.
So any one can give some criteria on my problem? Can I ignore it?
Very appreciated for your help!
Rilei Yu
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Received on Sun Sep 19 2010 - 20:30:03 PDT
