[AMBER] help in diffusion coefficient analysis

From: Robin Jain <robinjain.chem.gmail.com>
Date: Fri, 23 Jan 2015 13:32:40 +0530

Dear all,
As a test run, we are trying to compute diffusion constant of water.
We have taken 64 water molecules. I am confused about the "center" and
"image" command. Using the following command, we are getting the value
2.918 and without using the two commands we are getting a different
value (2.026). kindly suggest.

trajin X.mdcrd 1 last 1
unwrap :1-64
center :1-64 mass origin
image origin center familiar
diffusion 0.25 diff.out :1-64 average

Robin Jain
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Received on Fri Jan 23 2015 - 00:30:03 PST
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