Subject: summary: getting data from vibrational frequencies

From: "Joseph W. Bausch" <[email-masked]>
Date: Wed, 10 Mar 1999 18:36:25 -0500

Last night I posted the following to the CCL:

--------
I have an optimized geometry (using Gaussian94) of a highly symmetrical
molecule.  A frequency calculation indicates that it is a saddle point,
with 4 imaginary frequencies.  I have animated these frequencies using
MOLDEN.  I would like to reoptimize this structure "following" the changes
as indicated by each of the four imaginary frequencies (I'm hoping that it
will lead down to a transition state).  Is there any easy way to get
MOLDEN, or any other program, to give starting coordinates corresponding to
the geometries just slightly perturbed from this optimized geometry?
--------

As usual, the CCL community has been a big help!  It turns out that the
MOLDEN program does just what I need, as indicated below by the author of
MOLDEN.  The other responses I got are also quite informative, so I have
included them all.

Thanks to everyone that responded,
JWB

---
#1

From: Gijs Schaftenaar <[email-masked]>

molden has a commandline flag '-w opt' where opt can be 1 or 2,
'-w 1' will make molden write out a freqN.dat file with a series of xyz
geometries when you select a frequency, '-w 2' does the same only now
the file contains a series of mopac z-matrices. (molden can read these files
back in, now use the 'Select Point' section to display them).
The molden molden -d commandline flag will make molden print the equilibrium
geometry and the Normal Mode displacements.

Best Regards,

Gijs Schaftenaar

Author of Molden

---
#2

From: [email-masked] (Dr. Ida N. L. Ma)

Excel.  What you need is to get the geom in Standard orientation, and then
the displacement vector of the mode you are interested in:

        final displacement = original coordinate +(factor)*displacement vector

        where factor is a number, representing how much you want to
displace along the vector.  The small the number, the smaller the
displacement.

---
#3

From: Matthias Hofmann <[email-masked]>

Molecule can do what you ask for. This program was written for the Mac by
Nico Hommes who is at the University of Erlangen, Germany.
It allows you to specify how many pictures to be generated for the
animation and each can be used for generating a new input geometry.
In this way you can choose between a small or larger distortion.

But the program is not free.
For further information have a look at:
http://www.ccc.uni-erlangen.de/hommes/molecule/index.html

---
#4

From: Dmitry Khoroshun <[email-masked]>

Molecule for Macintosh by van Eikema Hommes can do some
steps along the specified directions.

---
#5

From: Pablo Vitoria Garcia <[email-masked]>

Viewmol will let you distort the molecule (and change the degree of
perturbation) and save the new coordinates. I send you as an attachment
some information about the program (which is freely available).

---
#6

From: Stefan Konietzny <[email-masked]>

there is a tool called xvibs. It produces a
trajectory xyz file out of a frequency output.
I use it with gOpenMol by Leif Laaksonen.
For a chosen vibration you can cut out the desired orientation and put it
back into your input, and hopefully the optimization goes down the hill.
If you like i can send you the source.

This is the beginning of the source:
xvibs
  version 4.0.1 (August 1997)

This program produces XYZ animation files for molecular vibrations
represented by normal modes taken from output files from Aces2,
Gamess, and Gaussian. The program autosenses what output file is
given. It writes separate files, one simple cosine trajectory for
particular normal mode. Vectors representing the normal coordinate are
attached to the atoms, which is useful for a static picture.

This program is not copyrighted. You are welcome to extend it,
or send your files to [email-masked] and I will gladly
extend it for you.

Send bug reports to: [email-masked]
-cut-
Written in 1990 by Milan Hodoscek
Institute of Chemistry, Ljubljana, Slovenia
Modified for XMOL 1992 @NIH, Bethesda, MD
Modified again Fred Brouwer Univ. of Amsterdam 1994
to include vectors ([email-masked] (Fred Brouwer))
Modified to accept G94, Yos Ginting ([email-masked])
Modified by Jan Labanowski, [email-masked] to accept input from GAMESS and
ACESS
Rewritten by Bradley A. Smith, (http://pollux.chem.umn.edu/~basmith/,
                                [email-masked])

---
#7

From: Elmar Gerwalin <[email-masked]>

I use xvibs to do exactly this.
xvibs is simple "C"-program , available as source code, but should be
easily to compile:
use:
cc xvibs.c -lm

See the file xvibs.c for further informations.
Now for the thing you need:

xvibs extrcats the normal modes from a g94-output and creates an
"xyz"-file (don't worry :-) ) for each mode you tell him.
(E.g. xvibs water.out 3    creates a file water.003.xyz
(or something like that) which contains a series of 20 (!)
cartesian coordinates for this mode.
So , first, programs that can animate xyz-files (like xmol) can show the mode
(like molden does)

second: you can cut out the 10th (NOT the last, because it's a loop:
the 20th is equal to the 1st) section of coordinates and use this as
NEW gaussian input !
This works fine when you want to follow 1 mode.

For more modes, I have no idea yet but to perform this procedure

Oh, xvibs is available (free) anywhere in the Web.
I don't know the Original source now, but you might find it at:
http://www.uni-duesseldorf.de/ftp/ftp/share/xvibs/doc/   or:
http://www.arl.hpc.mil/PET/cta/ccm/training/courses/scivis/xvibs/
or use a search engine..

---
#8

From: Karl Irikura <[email-masked]>

I have an awk script that will displace the geometry along a selected
normal mode.  It's attached; I hope it helps!

---
#9

From: "Stefan Fau" <[email-masked]>

you can create a distorted geometry by manually adding the vector of the
chosen vibrational mode to the coordinates as given in the Standard
Orientation. You can also use a small program called xvibs (available in
the CCL archive) for the same purpose.
It will produce a set of geometries that are distorted in varying
degrees (geoms for a "video"), but you can delete unwanted geometries.
I think you may get 6 numbers per line. In that case you are interested
in the first three numbers.

Alternatively you can use "molden -A" and the z-matrix editor (Gaussian
style). The "-A" prevents molden from reordering the atoms when creating
the new z-matrix. You can then alter the most important variables manually.

---
#10

From: "E. Lewars" <[email-masked]>

Hello, concerning your inquiry about the 4th-order saddle point:

I suppose you wish to relax it to a transition state (1st-order saddle) or to
a minimum. I don't know of a program that will *automatically* decrease the
symmetry and thus give an input geometry that when optimized will be a TS
or a min. You may be able to break the symmetry by inspecting the Cartesians
of your structure and then slightly altering a pair (or more than one pair)
and reoptimizing. If you have a good graphical interface like Spartan has,
you could alter bond lengths very simply in the builder, then reoptimize.
If you used a Z-matrix you can break the symmetry by making previously equal
parameters unequal.

---
#11

From: [email-masked]

Perhaps take the optimized structure coordinates R for which you calculated the
frequencies. One at a time add a small percentage of the FG eigenvectors
for each
of the four modes and reoptimize.

Recently I read an article on the optimization of tetramethyl silane with high
symmetry which was quite similar.  Turns out that using the keyword "tight"
eliminated the four imaginary frequencies and dropped the cymmetry to Cs
with no
imaginary frequencies.

---