Re: [AMBER] Aligning a trajectory

From: Jason Swails <>
Date: Wed, 17 Sep 2014 08:39:41 -0400

On Wed, 2014-09-17 at 08:20 -0400, Jonathan Gough wrote:
> Hey All,
> Is there a way to align or realign a trajectory to a reference frame? (I
> would assume using cpptraj) if so, can someone point me in the right
> direction?
> What I mean is. Could I align each sequential frame to say the first frame.
> That way I could run an analysis over the trajectory relative to a specific
> set of points in space.

That's what the "rms" command in cpptraj does (in addition to computing
the RMS deviation). You can even choose a subset of atoms to align to.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Sep 17 2014 - 06:00:04 PDT
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