Re: [AMBER] RMSD plot in ns

From: Reza Esmaeeli <>
Date: Sun, 20 Jun 2021 08:10:06 -0400

You can use a 0-20ns column in Excel for X axis. Or if generating your plot with matplotlib, simple use an array with ns values for X axis.

Reza Esmaeeli

> On Jun 20, 2021, at 07:58, Sadaf Rani <> wrote:
> ´╗┐Dear Amber users
> Could you please give me a suggestion on the following problem:-
> I have performed rmsd, rmsf, radius of gyration analysis on the trajectory
> from 20 ns simulation. A total of 2000 frames are saved in trajectory.
> However, I get the number of frames on x-axis instead of time as shown
> below. I used the following command for rmsd calculation:-
> rms tofirst :1-492.CA= first out rmsd1.agr time 0.01 mass
> How should I get time in ns instead of frames?
> Regards
> Sadaf
> [image: image.png]
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Received on Sun Jun 20 2021 - 05:30:02 PDT
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