Re: [AMBER] Rotation Matrix

From: David A Case <>
Date: Sun, 10 Oct 2021 08:29:21 -0400

On Sun, Oct 10, 2021, mohamed marzouk wrote:

>During my dissociation simulation for protein/DNA complex the system rotate
>(noticed during visual inspection), So I want to quantify this rotation.

If you are talking about the entire system (protein + DNA) rotating: that is
unlikely to be of much interest (aside from its use in estimating rotational
diffusion.) Even a non-dissociating system will rotate (and translate)
during MD.

>- How can I get the rotation matrix by CPPTRAJ from the reactive trajectory ?

Use the savematrices option in the rmsd command.


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Received on Sun Oct 10 2021 - 05:30:02 PDT
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