[AMBER] Eigenvector visualization in Nmode

From: JPB <jpb.q4md-forcefieldtools.org>
Date: Fri, 09 Dec 2016 16:32:36 +0100

Hi everyone,

I performed vibrational analysis on methanol with nmode from AMBER 12.
I used the following command:

nmode -O -i nmd-vec.in -o nmd.out -c nmd-min4.rst7 -p prmtop.parm7 -v nmd.vec

The different files (nmd-vec.in, 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 nmd-vec.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 nmd-vec.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
(http://mccammon.ucsd.edu/ied/) 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.

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Received on Fri Dec 09 2016 - 08:00:02 PST
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