[AMBER] Different result before and after AUTOIMAGE from CPPTRAJ?

From: Eg eh <egeh00.yahoo.com>
Date: Wed, 2 Sep 2015 20:21:50 +0000 (UTC)

Dear all,
I am using CPPTRAJ to calculate diffusion and mask. I found the results were different if I added "autoimage" in the script. I did not set iwrap in my MD input file. If I used VMD to check the trajectory file, I got an almost spherical water box. If I "autoimage" the trajectory file, I got a cubic waterbox. Which way is right for the calculation? I am really confused about how CPPTRAJ calculated for a PBC water box.
Thanks,
Xiaoquan.
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Received on Wed Sep 02 2015 - 13:30:03 PDT
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