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?
Thanks,
Jesse
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 05 2008 - 14:47:19 PST
