Re: [AMBER] PROTEIN-DNA rmsd plot

From: David A Case <>
Date: Wed, 16 Dec 2020 09:11:58 -0500

On Wed, Dec 16, 2020, Syeda Amna Arshi wrote:

>The .nc file of a protein DNA simulation of 500ns have 2500 frames when i
>plot the rmsd of the same by R for the protein it shows sudden fall at the
>equal intervals unlike rmsd plot for the only DNA doesn't show such
>pattern. I am attaching the protein rmsd plot as well as the R script to
>plot the graph.

Interesting use of "R"! But you should visualize your trajectories in a
program like VMD or Chimera to see what is going on. It looks like
something odd might be going on at restarts (was this trajectory
assembled from smaller parts?) Beyond that, one would need more
information to be of help.


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Received on Wed Dec 16 2020 - 06:30:05 PST
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