Re: [AMBER] Question about unusual RMSD behaviour

From: Amit Kumar <ak543714.gmail.com>
Date: Tue, 17 Sep 2019 14:44:25 +0530

I am really very sorry sir, I miswrote the question.
I found the RMSD value of the restrained system higher than the
unrestrained system, which is very unusual. I am also attaching the
result.

On Mon, Sep 16, 2019 at 6:57 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> 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 <ak543714.gmail.com> 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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system_compare.png
(image/png attachment: system_compare.png)

Received on Tue Sep 17 2019 - 02:30:02 PDT
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