Re: [AMBER] Eigenvector visualization in Nmode

From: The Cromicus Productions <>
Date: Fri, 9 Dec 2016 17:43:51 -0500

P.S.: I get normal modes with nab. You can find the code I'm currently
using in one of the latest posts (have to modify it a bit because I wanted
to impose constraints; without constraints that seemed to work)

On Fri, Dec 9, 2016 at 5:41 PM, The Cromicus Productions <> wrote:

> 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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