[AMBER] Rotation Matrix

From: mohamed marzouk <mohamedmarzoukphysics.gmail.com>
Date: Sun, 10 Oct 2021 10:58:13 +0900

During my dissociation simulation for protein/DNA complex the system rotate (noticed during visual inspection), So I want to quantify this rotation.
To do so, I want to get the rotation matrix that used after alignment to calculate RMSD, form this (Rotation matrix) I can get the angles of rotation.
My Q’s?
- Is this right way to quantify the rotation or there are other suggestions ?
- How can I get the rotation matrix by CPPTRAJ from the reactive trajectory ? Any tutorial or things to follow?
- From Rotation matrix how can I get the angle ?

Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.

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Received on Sat Oct 09 2021 - 19:00:03 PDT
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