Subject: Summary:molecular modelling workshop

From: Dermot Brougham <[email-masked]>
Date: Mon, 22 Jan 2001 08:42:11 +0000

A couple of weeks ago I asked a question about running a molecular
modelling workshop, thanks to all who replied. The original question and
summary are below.
Sorry about the delay

Original question:
>I am currently applying for funding to run a workshop in molecular
>modelling for our 4th year group (40 students). I plan to give 4-5
>lectures and then have a series of workshops (maybe 4x3 hours) with
>progressively less supervision as time goes on. Ending up with the
>students picking a problem of their own (probably from their organic
>chemistry lectures) and tackling it using whatever methods they see as
>fit and then writing a short report. Maybe the people who read the CCL
>have done something similar. I would be grateful for any advice,
>particularly about:
>Software: Best? Value for money?
>Hardware: Do you need a PC each or can you have them in pairs,
>threes....?
>Pedagogy:
>Has there been much published on this type of course?
>What are the major issues?
> Does the course I have outlined make pedagogical
>sense?
>Or is there a superior alternative approach?

Replies:
The consensus is that Spartan is the best software
Andreas Ehlers replied
"It provides a very good GUI and contains all the methods from MM, semi
empirical to ab initio, so
the students don't have to change programs and write specific inputs for

each problem. But it is expensive."
Yes cost is the problem here, several others agreed with Andreas.

Among the free options were MOE, recommended by David ENOT
"Recently, I ve seen a demonstration of MOE which seems to be
advantageous : you can perform classical modeling tasks as well as drug
design in a
highly pedagogical way, all the platforms are supported and it's free
for education.
Have a look at http://www.chemcomp.com "
I haven't had a chance to try it yet.

Also free is
WebMolecules
Over 200,000 Molecular Models Online in Full 3D
http://www.webmolecules.com
Requires 3D plug-in. Indexed and searchable.
Although this isn't quite what I was looking for myeself!

For a little more money:
Molecules-3D
3D Molecular Model Building
http://www.molecules.com/m3d25int.shtml
Great for new students. Only $49

Molecules-3D Pro
3D Molecular Modelling
http://www.molecules.com/m3d25int.shtml
Ideal for students interested in Computational Chemistry. $99
As recommended by John Vermeer

Several people from MSI contacted me talking about Materials Studio
"http://staging.msi.com/materials/studio/
Or if you wish to evaluate a copy of Materials Visualizer:
http://staging.msi.com/materials/studio/quote/"
I have yet to try this!

Several respondants recommended third party individuals who have run
workshops, I am
in the process of contacting these people, I won't give their names as
they haven't replied yet.
But if they throw up any nuggets I will inform the CCL.

In terms of pedagogy there appears to be many ways to teach MM
successfully,
thanks to Hens Borkent, Michael Nolan and others here.
Most replies suggested that what I had outlined will work, but that it
is
very important to keep the groups small (stagger the sessions if
necessary).
People disagreed as to whether one or two per PC is best, probably two
if the students are
"general chemists". It was agreed that you should never have more than
two per PC and also
that the course should be short if it is for general chemistry,  i.e. 2
or at most 3 weeks.

What Hens said was good:
He uses "a web interface to mopac calculations, based on the Chime
plugin, as you can find under
http://www.cmbi.kun.nl/wetche/organic/
It requires W95/98 Netscape 4.5 - 4.7 to function properly, in
particular the 'editor'. On the editor page you will also find
suggestions for
exercises. Since this is not really a modelling course, a number of
input files
have been constructed beforehand, and the students simply submit them,
but they can also edit the files if they want to.
On practical questions:
We prefer them to work in pairs, which forces them to discuss the
subject among eachother, talk about it. Three people with one mouse is
too many.
It is nice indeed to have a goal in the end: either a kind of
competition, who comes up with the best figures, lowest minimum, etc.,
or a
presentation, in Powerpoint or HTML (chime), as you propose.
It is also our experience that courses of this type should not take too
long. There should be regular interrupts, classical lectures etc,
otherwise
they start "playing" with the computer, chatting, e-mail, browsing.
The main goal is to keep them interested in the subject, add the right
amount of interactivity to keep them busy for a while, then have a
break and get the group together in a discussion of the results.
Sometimes you have luck if you ask them to suggest their own problems,
but it is wise to have some problems at hand. I noticed that many
organic chemists work on very large molecules these days, biological or
supra-
molecular, that are not so easy to model."

One follow up question, I was expecting that Tinker would be mentioned,
but it wasn't;
Tinker is free; is it any good? Easy for students? GUI?

        Thanks again
                    Dermot

--
Dr. Dermot Brougham,

School of Chemical Sciences,
Dublin City University,
Dublin 9,
Ireland.

Tel:  353 1 7005472
Fax:  353 1 7005503