CCL:G: How to visualize normal modes
- From: Steve Williams <willsd:appstate.edu>
- Subject: CCL:G: How to visualize normal modes
- Date: Sun, 21 Oct 2018 11:07:44 -0400
I wrote a program a long time ago that read the equilibrium cartesian
coordinates and cartesian displacements from a modified gaussian output
file, that would then generate a series of displaced geometries by adding
something like -1.0*displaced x coord to equilibrium x coord and so on for
all coords of all atoms, then -0.90*displaced x coord to equilibrium x
coord, through 0.10**d*displaced x coord to equilibrium x to 1.0**displaced
x coord to equilibrium x coord and so generate 21 new structures each with
a different displacement along the selected normal mode. I used an ancient
vizualization tool called xmol to animate these. I do recall there was some
small controversy about how the displacements that gaussian printed out
were normalized, but I am no linger sure of the details on this. There is
a small chance I still have this fortran code somewhere but it has been
more or less 20 years ago.
Steve Williams
On Sun, Oct 21, 2018 at 7:05 AM Mark Andreww Zottola mzottola ~~ gmail.com <
owner-chemistry .. ccl.net> wrote:
>
> Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com]
> I can use any of a number of good visualization software to observe the
> normal
> modes from a qm calculation. However, if I want to generate a series of
> structures from that normal mode calculation, I receive the frequency, the
> intensity of the transition and a set of cartesian displacements.
>
> It is the last that I do not understand. Given the equilibrium geometry,
> what
> should I do to generate coordinate files? Are these vectors to be added
> together? Or are these meant to be a cross product? Perhaps something
> else?
>
> I just want to consider creating a multi-conformer file based on normal
> modes.
> I am simply looking for a direction in order to move forward.
>
> Thanks.>
>
>