Re: [AMBER] Eigenvector visualization in Nmode

From: David A Case <>
Date: Fri, 9 Dec 2016 21:25:40 -0500

On Fri, Dec 09, 2016, JPB wrote:

> Now I have difficulties to visualize the eigenvectors which are written out
> in the nmd.vec file.

Both IED and nmode are ancient programs. For VMD, check out the normal mode
wizard (just Google on that). cpptraj can create wizard-compatible files
for principal-components or quasiharmonic modes:

If you can grok the format that the normal mode wizard needs, you can probably
convert a vecs file to that. Some enterprising Amber developer could do a
good deed by adding the option to write that format into NAB's nmode()


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Received on Fri Dec 09 2016 - 18:30:04 PST
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