Re: [AMBER] Question about unusual RMSD behaviour

From: Carlos Simmerling <>
Date: Mon, 16 Sep 2019 09:26:55 -0400

Yes this is very sensible. I would expect that the restraints would keep
the structure closer to the initial model (if that's what you use as the
reference for rmsd), leading to lower rmsd with the restrained trajectory.

On Mon, Sep 16, 2019, 9:20 AM Amit Kumar <> wrote:

> Dear Amber users,
> I ran a simulation of a fibrillar protein for few nanosecond (with and
> without torsional restraint) using Amber16. I used implicit solvent (igb=5)
> results when analysed in terms of RMSD, the RMSD value of the unrestrained
> system was higher than the RMSD value of the restrained system. Is it
> possible? Can you explain the phenomenon?
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Received on Mon Sep 16 2019 - 06:30:04 PDT
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