Hi,
You can use rms fit command, as it discards the translation and rotational motions present.
Satyajit Khatua
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________________________________
From: Cenk Andac via AMBER <amber.ambermd.org>
Sent: Sunday, October 16, 2022 12:45:34 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] "autoimage" function of cpptraj and holding molecule steady
Dear Amber community,
I used the "autoimage" function of cpptraj to re-image a molecule in my MD
trajectory. Indeed, the "autoimage" function does a pretty good job as
compared to the "image" function of cpptraj.
As expected, the molecule is well centered when I visualize the trajectory
by UCSF chimera. However, the molecule seems to rotate around the center of
the box. I can keep the molecule steady by Actions>Hold Selection Steady
command in UCSF Chimera.
I was wondering if cpptraj has a parameter that does a similar job as
Chimera to hold the molecule steady in the trajectory.
Best,
Cenk Andac.
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Received on Sat Oct 15 2022 - 13:00:02 PDT
