Hello,
Someone else asked a very similar question recently....
try this:
center origin .CA
image origin center familiar
rms first .CA
The rms command will make it easy to see water near a point on your protein.
-Trevor
________________________________________
From: Ye MEI [ymei.itcs.ecnu.edu.cn]
Sent: Sunday, September 19, 2010 8:02 PM
To: AMBER Mailing List
Subject: Re: [AMBER] molecular dynamics simulation-water-box-diffution problem
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 Tue Sep 21 2010 - 22:30:07 PDT
