Re: [AMBER] RMSD plot in ns

From: Dr. Anselm Horn <>
Date: Mon, 21 Jun 2021 09:11:27 +0200


as a short add-on - since you seem to use xmgrace for your plot:
Even if you just have the snapshot number as x-axis, you can simply
"transform" it to the appropriate time, since you know the conversion

For example, if you wrote snapshots every 10 ps, did not specify any
time information, but you want to present your plot in ns, in xmgrace
you open the 'Plot' ->' Axis properties' window, select the tab 'Tick
labels' and enter in the field 'Axis transform':
where $t represents the variable for the actual axis value you like to
transform. So you can easily change the graph plot without changing the
input data.

Best regards,


On 06/20/2021 04:22 PM, Daniel Roe wrote:
> Hi,
> Based on the plot it looks like you do indeed have time in ns (it goes up
> to 20 as desired), it’s just the label that hasn’t changed. Try adding
> ‘xlabel Time’. Or just change the x axis label in grace.
> -Dan
> On Sun, Jun 20, 2021 at 7:58 AM 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 Mon Jun 21 2021 - 00:30:02 PDT
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