[AMBER] Regarding the visualization of the nmd file after pca in VMD

From: Sruthi Sudhakar via AMBER <amber.ambermd.org>
Date: Sat, 25 Feb 2023 19:25:49 +0530

Dear all,

I have carried out PCA in AMBER and generated the NMD file to observe the
movement and generate the porcupine plot in VMD. When I open the nmd file
into VMD, the arrows of a particular domain are pointed towards one side.
However, once we play the animation of the particular mode, the movement
seems to be in the opposite direction. Why does this happen? Is there
something that we are missing or wrongly doing? The direction of arrows can
be altered by the +/- option, but is that the right way?

Kindly help and provide suggestions.

Sruthi Sudhakar
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Received on Sat Feb 25 2023 - 06:00:03 PST
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