AMBER Archive (2008)

Subject: AMBER: Ptraj Normal Mode Analysis

From: Jesse Jun (
Date: Fri Nov 14 2008 - 15:19:31 CST

Hi All,

I'm doing ptraj normal mode analysis on a simulation, and I would like
to show the dynamics during this simulation. Once I get the output
file (in this case, I have run a mode analysis of displacements of
cartesian coordinates along mode directions) as pasted below, I am not
sure how to visually represent this data. Here is what I get as an
output file:

Analysis of modes: DISPLACEMENT
   Atom no. displX displY displZ
          1 6.888 -3.719 8.146
          2 5.762 -3.005 6.630
          3 5.425 -2.620 6.335
          . . . .
          . . . .
          . . . .
          2020 8.590 -4.526 5.623

I have tried the ptraj "projection" command, in which snapshots are
projected onto modes, but I get the following message with no
additional data that can be visualized:

Projection of snapshots onto modes
   Snapshot Mode7

Is there something like a porcupine plot, or something similar, that I
might be able to generate with this format of data? Does anybody know
how I might be able to do this?

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