Re: [AMBER] calculation of rmsd with cpptraj

From: Krantzman, Kristin D <>
Date: Mon, 17 Aug 2015 20:15:08 +0000

Dear Jason,
Thank you! You explained this very well!
Best, Kristin

-----Original Message-----
From: Jason Swails []
Sent: Monday, August 17, 2015 4:03 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] calculation of rmsd with cpptraj

On Mon, Aug 17, 2015 at 3:53 PM, Krantzman, Kristin D <>

> Dear All,
> I have a puzzle that I do not understand. I have a system with 5
> molecules that have resid's 1, 2, 3, 4 and 5. When I select one
> residue and have cpptraj calculate the rmsd for a trajectory, the
> value is very small at all time steps, i.e. rms :1 out res1.rms. I
> get a small value for all time steps for all the residues, i.e. rms :2
> out res2.rms, etc. However, if I calculate the rms for all of the
> residues (five total) collectively, i.e. rms :1-5 resall.rms, the
> value of rmsd is much larger and increases over time. Could anyone
> explain this discrepancy? I have this when I do the calculation on a
> wrapped trajectory and also when I include the keyword noimage. I have
> searched through the Amber archives and reference manual, and I cannot figure out what is incorrect.

‚ÄčNothing is incorrect -- this sounds exactly like what *should* happen.
When you do an "rmsd" command in cpptraj, it automatically applies a translation and rotation that minimizes the requested RMSD (unless you use the "nofit" keyword to prevent this).

When you do each molecule independently, it will translate each frame and rotate them to minimize the RMSD. For a single molecule, this completely eliminates the effects of translational and rotational diffusion.

However, when you have *multiple* molecules in your RMSD fit, the translation and rotation eliminated by the fit is for the *combined* system of all selected molecules. However, their translations and rotations *relative to each other* cannot be eliminated. As a result, the RMSD appears much larger in this case. Furthermore, the longer the simulation runs, the more these molecules diffuse, so the larger the RMSD will become. What you're observing here is basically the difference between considering and ignoring diffusion in an RMSD calculation.‚Äč


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 17 2015 - 13:30:06 PDT
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