Subject: CCL: vibrations animation (summary)

From: [email-masked] (Godbout Nathalie)
Date: Mon, 28 Aug 1995 10:49:22 -0400 (EDT)

Hello everyone,

I wish to thank the many CCL members who answered
my request. I should have mentionned that the calculations were
done with deMon. I am providing a summary of the responses.
I have already tried Molwin. I can send the long version
of the answers to anyine who is intrested.
Again, many thanks, you have been very useful. 

Nathalie

> 
> 
> Hello CCL members,
> 
>   I am in need of a program that will help me visualize 
> the nature of the calculated normal modes of molecules. 
> Specifically, the commonly found illustrations of arrows 
> along bonds would be helpful. The molecules contain 
> between 20-25 atoms, hence the difficulty in interpreting 
> the results of the vibrational analysis. 
> 
> Many thanks in advance for your help.
> 
> Nathalie 
> 

From: "Richard Bone" <[email-masked]>
----------------------------------------
Cache Scientific visualisation interface 

From: "E. Lewars" <[email-masked]>
----------------------------------------------------
Molwin 
  ->you can find it at oak.oakland.edu/simtel/win3/chem/molwin23.zip
    Dr Pavel Ganelin wrote the program

From: "Igor Baskin" <[email-masked]>
---------------------------------------------
HyperChem 

From: [email-masked] (Cory C. Pye)
----------------------------------------
I believe some of the programs in the GAMESS-US distribution can do this. A 
better solution in my opinion is to use Gaussian 9X to calculate the vib. 
modes and then use a program called xvibs or viban to extract the modes from
the output. These produce animation files (Cartesians) which can then be
read by XMol (1.3.1). 

From: [email-masked] (lee wilson)
-------------------------------------------
Serena Software, Box 3076, Bloomington, IN 47402-3076, has a
program, PCM-Vibrate, that takes MOPAC or Gaussian output and displays the
normal modes in the way you describe. Academic price is $200. 

From: [email-masked] (Joel Polowin)
--------------------------------------------
Our HyperChem software can do this.  After performing a semi-empirical
calculation on your structure, it can do a vibrational analysis.  This
lets it display the "arrows" that you describe; more usefully for many
people, it can actually animate the various vibrational modes so that
one can see the structure wobbling according to each mode.
I can send you more information about HyperChem if you wish; we can
send you a package of brochures and demo disks.
The demos are also available from our ftp server, ftp.hyper.com, in the
directories under /pub/demo .  They can also be obtained from our WWW
server, http://www.hyper.com .

From: [email-masked] (Joseph W. Bausch)
-----------------------------------------------------
Check out the program Gamess and an associated program ("Molplt").  This
might be one way of doing it.  It is available free of charge.  Do a net
search for "gamess" and you will get the info you need.  I think the web
site for info is the following:
http://www.msg.ameslab.gov/

From: [email-masked] (Brett Bode)
-----------------------------------------
If you have a Macintosh then you might find my program, MacMolPlt, useful.
It displays molecules with, or without normal modes, in 3D and rotates and
animates the modes in real time. It also produces good quality output via
direct printing or copy and pasting into another application. It is
oriented towards output from the GAMESS program, but it is not difficult
to create an input file with the coordinates and modes.
If you are interested in MacMolPlt you can get more information and/or 
download the program using anonymous FTP to www.msg.ameslab.gov
or via the WWW using the URL 
http://www.msg.ameslab.gov/GAMESS/Graphics/MacMolPlt.html

From: Pisanty Baruch Alejandro-FQ <[email-masked]>
-----------------------------------------------------------------
if you have access to Silicon Graphics and Cray computers, UniChem does a 
fine job for what you appear to need. It will actually give you a motion 
picture of the vibrations.

From: "Andy Holder" <[email-masked]>
------------------------------------------
Our AMPAC 5.o with Graphical User Interface visulaizes the computed vibrations 
from one of the semiempirical methods included in AMPAC as well as from a 
Gaussian calculation.  If you would like, I will be happy to send you a 
brochure.  

From: "Wayne Huang" <[email-masked]>
---------------------------------------------
Spartan can visualize the vibration from the calculated normal modes and
also build vibration sequence for animation. Product info: [email-masked]

From: [email-masked]
---------------------------------------
I saw a program called CERIUS2 being demoed at a physics conference a few 
months ago. Part of it did contain a tool for visualising vibrations of 
molecules. You clicked on a peak in a vibrational spectrum and the molecule
on the screen actually bent and wobbled according to that mode. 

From: Magan Govender - PG <[email-masked]>
--------------------------------------------------
We have the programs called Vibram, which requires the Gaussian
Eigen value matrix and displacement coordinates from the freq
calc. There is also a much more user friendly program called
vibratio, which is free from ftp www.ccl.net, in the
pub/chemistry/software dir....This program also requires
the Gaussian freq output file.

From: "E. Lewars" <[email-masked]>
----------------------------------------------------
Hello,   Sorry I didn't mention that MolWin animates frequencies using the 
output of Gaussian.  It will also depict the molecule given Cartesians (but
of course in that case there are no freqs).  Since you are not using 
Gaussian, if you wish to try to animate the freqs with MolWin, you must
transform your output so that it resembles Gaussian enough for MolWin 
to accept it.  If MolWin seeks a keyword then a certain format of freqs and
their displacements, it should be possible to modify your output accordingly.
However, I do not know if this will be practical.  
  I suggest you discuss the problem with someone in your department, or
contact Dr Pavel Ganelin, the author of MolWin.  You probably have someone
in your dept who uses Gaussian and can give you a sample freq calc output
(I know MolWin works with Gaussian 92; probably it also works with G90 and
G88).  If not, I should be able to send you an example of Gaussian  output.
-- 
------------------------------------
|Nathalie Godbout                   |
|Universite de Montreal             |
|Departement de chimie              |
|C.P. 6128, Succ. Centre-ville      |
|Montreal, Quebec  H3C 3J7          |
|Canada                             |
|Tel: (514) 343-6111 ext. 3949      |
[email-masked]        |
------------------------------------