Re: [AMBER] Eigenvector visualization in Nmode

From: The Cromicus Productions <>
Date: Fri, 9 Dec 2016 17:41:23 -0500

I had the same problem a couple of weeks ago. My solutions were not the
best ones but they worked:
- I installed IED indeed, but in my case the visualization was not very
helpful (displacements were kind of small, at least in my case)
- Then, I did a code in python which adds/substracts the eigenvector (or a
multiple) a certain number of times, and defined a trajectory with that.
Then, I visualized the trajectory in vmd.
Hope someone can come up with a better solution, but if not, my way seems
to work.

On Fri, Dec 9, 2016 at 10:32 AM, JPB <> wrote:

> Hi everyone,
> I performed vibrational analysis on methanol with nmode from AMBER 12.
> I used the following command:
> nmode -O -i -o nmd.out -c nmd-min4.rst7 -p prmtop.parm7 -v
> nmd.vec
> The different files (, nmd.out, nmd-min4.rst7, prmtop.parm7,
> and nmd.vec) are attached to this message.
> Now I have difficulties to visualize the eigenvectors which are written
> out in the nmd.vec file.
> First, if ivform=1 in, (eigenvectors are to be written in
> formatted form), the nmd.vec file remains empty and I don't understand what
> goes wrong here.
> Second, if ivform=0 in, (eigenvectors are to be written in
> unformatted form which is the case of the example in this message), I am
> not sure of the way to visualize them.
> It seems the IED (Interactive Essential Dynamics) software (
> can be used to handle the nmd.vec but it
> was developed to run with older version of VMD and Numeric library for
> Python. I am kind of reluctant to get into compilation and installation of
> previous version of VMD and Python. I am wondering if I did not miss a
> better and easier way to visualize the eigenvectors.
> In short:
> Why is the nmd.vec file empty when ivform=0?
> What would be a smart way to visualize the eigenvectors?
> Your help and insight would be greatly appreciated.
> Cheers
> JP
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Received on Fri Dec 09 2016 - 15:00:02 PST
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