animation
Sorry for the delay, but here is the summary of responses to my post
requesting information about animation. Thanks to everyone who responded!
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Post:
Hello Netters,
I am wondering how many of you have used animation as a teaching or
research tool. What platforms and software are available to do this sort
of thing besides Cache? If you had the ability to make an animation on a PC
by
stringing together coordinate files (like Macromodel or Xmol) what would
you want to display? Dynamics simulations? Gaussian vibrational modes?
Reaction Mechanisms? Would the ability to do this on a PC be useful?
Thanks in advance. Responses will be summarized and posted if
this request generates sufficient interest.
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Responses:
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From: Joe M Leonard <jle[ AT ]world.std.com>
AVS has the components needed to animate various chemical things, and several
demonstration modules showing structural animation were developed 1-2 years
ago. Contact Doug Smith at UToledo for additional information, although
there are others that worked in this area.
The version of SPARTAN currently scheduled for Xmas or so will have the
ability to animate structures and mo's and the like. The prototype has
been demonstrated for several months, but we were unable to get into
the Version 3 release currently being beta tested.
I imagine that animation can be done in Explorer as well - contact Henry
Rzepa, who has done a bunch of work in this area as I recall (net traffic).
Joe Leonard
jle[ AT ]world.std.com
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From: Dongchul Lim <lim[ AT ]rani.chem.yale.edu>
What I would animate is trajectories from molecular dynamics calculations,
intrinsic recation coordinates and vibratinal modes from gaussian or
mopac calculations, motion of solutes and solvents in statistical
thermodynamics simulations, etc.
I guess HyperChem for MS-Windows is capable of some of these animations
(on PC).
-DCL
Department of Chemistry, Yale University
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From: Norbert Mueller <NMUELLER[ AT ]EDVZ.UNI-LINZ.AC.AT>
The new version (3.5) of Ball & Stick, the molecular graphics package for
Macintosh I have been developing, can create QuickTime movies from static
moving structures or from a series coordinate files resulting from an MD
run.
Ball & Stick is availble from
Cherwell Scientific Publishing
15 Auburn Place
Brookline MA 02146
Tel: (617) 277 4200
Fax: (617) 739 4836
or
Cherwell Scientific Publishing
The Magdalen Centre
Oxford Science Park
Oxford OX4 4GA, UK
Phone +44 (865) 784 800
Fax +44 (865) 784 801
or
Cherwell Scientific Publishing
c/o CHEM Research GmbH
BeethovenstraBe 7b
D-60325 Frankfurt 1
Tel: +49 (069) 4711114
Fax: +49 (069) 740496
A free demo should appear on info-mac and the michigan archives any tome now.
Hope this helps
Norbert Mueller
Institut fuer Chemie
Johannes Kepler Universitaet
A-4040 Linz
Austria
e-mail:
NMUELLER[ AT ]edvz.uni-linz.ac.at (preferred)
norbert[ AT ]soft.uni-linz.ac.at
NorbertM (AMDA-Link Linz) ->FirstClass
K360171[ AT ]alijku11.earn \
K360171[ AT ]alijku11.bitnet > will expire in 1994
K360171[ AT ]alijku11.edvz.uni-linz.ac.at /
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From: SBPM Marc GINGOLD <marc[ AT ]david.saclay.cea.fr>
We use for research the animation in QUANTA on RS/6000.
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From: Henry Rzepa <h.rzepa[ AT ]ic.ac.uk>
We are using animation modules developed using Explorer 2.0 to
display vibrational modes, orbital transformations etc. This is done on
SGI. We then convert to Quicktime format, which can be played on
Mac or PC.
Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY;
rzepa[ AT ]ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869.
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From: Phil Bays <pbays[ AT ]saintmarys.edu>
I use an SGI Indigo with Spartan from WaveFunction, Inc. or LabVision from
Tripos. With LabVision, I can do dynamics and "illustrate" the
rotational
barrier in Butane in a dynamic way (or any other molecule, for that matter).
With Spartan, I can do normal mode calculations and display vibrational
frequencies. I can also show HOMO's and LUMO's and therby illustrate
reactivity, though that is not yer available in a dynamic way. I
Understand that the new version of Spartan, due out the end of the month,
will allow that.
I also use a product put out by Falcon Software in Vt. called Organic Reaction
Mechanisms and running on a Mac. It illustrates dynamically most of
the standard reactions you want to look at in an organic course. This
was put together using MacroMind Director, I thnink.
Obviously, I am an organic chemist and teach in an undergraduate college
situation. I sue all of these in my sophomore organic course. By the
end of the year, thanks to an NSF ILI grant, we will have sufficient
workstations that I can give students assignments on the computers, not
just use them for classroom demos.
Phil Bays
Saint Mary's College
Notre Dame, IN 46556
(219) 284-4663
pbays[ AT ]saintmarys.edu
bays[ AT ]indigo.saintmarys.edu
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From: Barry Rowe <browe[ AT ]ncsa.uiuc.edu>
Matt,
We here at the NCSA ChemViz group use animations extensively. We use
either NCSA Collage or NCSA Image to animate calculated images to show
changes in molecular shape as atoms approach or move apart.
We are developing curricular materials for high school Chemistry teaching.
Our most useful animations are slices through the centers of (some) of the
atoms in a molecule as bonds are formed. We also use graphs of the lowest
energy of the total system to determine bond length (and sometimes bond
angle). Our images are calculated with NCSA DISCO on a Cray.
If you have any questions, please contact me.
barry
[] [] [] [] [] [] [] [] []
Barry E. Rowe browe[ AT ]ncsa.uiuc.edu
NCSA ChemViz group
240 CAB, 152 E. Springfield Ave.
Champaign, IL 61820
ANY PRACTICAL APPLICATION OF
PHYSICS OBVIOUSLY INVOLVES
MATTER, AND IS THEREFORE
CHEMISTRY.
[] [] [] [] [] [] [] [] []
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From: Richard Gillilan <richard[ AT ]chroma.tc.cornell.edu>
>
>
> Hello Netters,
> I am wondering how many of you have used animation as a teaching
> or research tool. What platforms and software are available to do this
> sort of thing besides Cache?
I use IBM Data Explorer. I'm about to release a suite of chemistry
modules designed for molecular modeling with emphasis on animation
production. I'll announce to the list when available (next couple
of weeks). In practice we find that DX is quite a good tool for
education (about the use of graphics). When it comes to actual
simulation, something like Hyperchem or macromodel may be better.
>If you had the ability to make an animation
> on a PC by stringing together coordinate files (like Macromodel or Xmol)
> what would you want to display? Dynamics simulations? Gaussian
> vibrational modes? Reaction Mechanisms? Would the ability to do this on
> a PC be useful?
Most requests I get are for videos used in conference presentations,
although recently one of my clients had a request for a tape to
be used in a biophysics class. The subject is normal-mode vibrations
of proteins (G-Actin in this case). I'd like to see more of this,
but some argue, and justifyably so I think, that video is not a
very good medium for education. Students have no chance for interaction
or to ask questions and get more detailed explanations or to get the
information at a slower pace. Interactive multimedia might be better,
but then why not just let them play with the actual data using a modeling
program?
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stereo pair stereo pair
Richard E. Gillilan
H H H H Visualization Specialist
\ | | \ Cornell Theory Center
H--C---C--H H---C---C---H richard[ AT ]tc.cornell.edu
/ | | / (607) 254-8757
H H H H
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From: Williams Brian W <williams[ AT ]coral.bucknell.edu>
Dear Mr. Stahl: You might want to consider contacting John Ranck at
Elizabethtown College (ranck[ AT ]vax.etown.edu) for possible uses of animation
in teaching applications. John is heading up a group of several small college
professors called the "Molecvue Corsortium" which is trying to use the
advances in computational chemistry to develop and improve teaching tools.
Although I have just inititated active contact with this group, they
appear to be focussing on using programs such as Hyperchem , Gaussian and some
commercially available animation products to further teaching goals.
Perhaps you could get some ideas/insight from him, or other members of
this group. Best, Brian Williams
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From: WILLSD[ AT ]conrad.appstate.edu
Matt:
I have recently used animations in a way similar to you interests.
I had a student in need of a programming problem and suggested that
he write a filter program that reads a g92 freq output file and
generates from it sequence of .xyz images that can be animated in
xmol. I used this in my physical chemistry class to show the
students what normal modes look like, and why they have the
symmetry designations that they do. It was effective, but rather
cosy: we do not have facilities for this in classrooms, so I had
all of the students crowd in my office to look at my screen. Luckily
there were only 9 students.
I would be interested in hearing what sorts of responses you get,
especially if those responses describe the hardware used to display
animations in the classroom.
Thanks,
Steve Williams
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From: CHAMH[ AT ]INDSVAX1.INDSTATE.EDU
Matt:
I am familiar with a very nice utility, KGNGRAF, which operates
on the RS/6000 platform. It accepts files from GAUSSIAN, MOPAC, and
HONDO and can perform animations of the normal modes, as well as provide
a schematic IR (RAMAN) spectrum. MO diagrams and van der Waals surfaces
(among other nice features) are also represented. KGNGRAF is written by
Steve Chin (IBM/Kingston).
Arthur M. Halpern
Department of Chemistry
Indiana State University
Terre Haute, IN 47809
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From: uchjs%earth.dnet[ AT ]terra.oscs.montana.edu
Sounds like a great idea. I have written an MD program that runs on a PC and
displays a 3D picture in "real time". It only handles spherical
force-field
atoms, however. I have used it nonetheless to illustrate collision dynamics,
vibrations, rotations, unimolecular dissociation and surface (and cluster)
impact processes (sputtering). It should be easy to adopt to simple reaction
dynamics, A + BC = AB + C.
I strongly believe that simulation/animation will be a great teaching tool.
For one thing, it allows for active input from the students as they can easily
change parameters and see the effects. The main problem is practical -
most lecture rooms do not have the equipment at hand.
If market issues are your concern, you may want to take a look at a recent
article (May??) on trends in the textbook market in the Wall Street Journal.
Give me a message and I'll find you the date of the article.
By the way, what is Cache??
Jan Sunner
Chemistry
Montana State University
UCHJS[ AT ]MTSUNIX1
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From: Leland Wilson <lwilson[ AT ]polaris.lasierra.edu>
My guess is that PC's are more accessible to more people than are the
Mac's for which Cache is designed. Now that prices are more reasonable
486's are going to be more plentiful. Any animation would be useful
especially in teaching. lee wilson, Chem. Dept., La Sierra U.
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From: Louis.Grace[ AT ]um.cc.umich.edu
Dear Matthew,
A former graduate student in my group and I (currently a graduate
student) have performed quite a few GaussianTM frequency calculations.
To aid in ascertaining which mode is which, we have been visualizing
the molecules as they are displaced for each mode. We have been using
a program called Molecular Editor to do this. The version of Molecular
Editor which we have runs on a Macintosh. I do not know if there is a
PC version available. (I believe it's freeware, but I'm not sure. It
was written at Drexel University.) Molecular editor does perform
animation by switching back and forth between two files (which contain
the coordinates of the atoms at the positive and negative displacements
from equilibrium).
I have had to go outside our lab to do this, as our lab has only
PC's! It might be desirable to have a program for the PC to do this.
I thought this might interest you.
Louis Grace
Department of Chemistry
The University of Michigan
Ann Arbor, Michigan 48109