Subject: Response to request for learning programs

From: [email-masked] (Barry J. Hardy)
Date: Tue, 12 Jul 94 00:56:00 -0400

CCLers,
     I enclose below my original post for 1) interest in a particular
learning program MCMD1D and 2) gathering a list of learning programs.
As one might see from the summary of responses I failed to gather
a good set of responses to 2) in terms of actual programs. 
I did receive the sugestions though of where to look (osc,
QCPE, basic textbooks, etc.). The job remains to be done though
(he says as he heads off on a trip tomorrow, :) ). Perhaps the
recent suggestion by Herbert Homeier is relevant here.
We need a Guide to Available Chemistry Software (GACS) Project.

     Also, my experiences agree quite well with Robert Topper's comments.

     Getting back to 2), I would summarize the situation for
finding/using comp chem programs as teaching tools:
a) Work with books such as:
     Allen & Tildesley & its programs
     Warren Hehre & its programs 
     Numerical Recipes & its routines 
     Lipkowitz & Boyd
b) Scour QCPE, osc, archie, gopher sites etc.; i.e. dig around 
[How many CCLers out here recently got no 'work' done one evening
because of reading their email, browsing in loops around the Web 
or searching through endless hierarchical gopher site menus; :)]
c) Standard Packages, Dig around for scripts  

     On 1) I have decided to make the program available directly 
on a testing basis and later through QCPE, osc and anon ftp.

Enjoying the Net connection,
Barry J. Hardy

**********************************

     ORIGINAL POST

1) I developed a relatively simple program MCMD1D for a recently
published paper (B.J. Hardy & R.W. Pastor, J. Comp. Chem., 
15, 208 (1994)); simulations using the program are described
in the Appendix.). The program allows one to study the application of
Monte Carlo and Molecular Dynamics algorithms to simple one 
dimensional functions. I am currently musing on the program's fate.
(The program is not robust software neither does it have any
fancy graphics interface.)
My question to CCLers is thus: 
"Is there any interest in using the program as a learning/teaching tool
and if so what are your requirements to make this useful?". 

2) What programs are out there that cover the basics of computational
chemistry techniques? I volunteer to summarize a list of programs 
back to CCL based on contributors' suggestions. A brief description
of its distribution/availability, price if commercial, method(s)
covered, references etc. could be included with the program suggestion.

**********************************

     SUMMARY OF REPLIES RELATED TO 2)

Don't overlook the tutorials that come with most of the major
commercial packages.  I hear that Biosym's is particularly good
and I know that Tripos is working on updataing some of theirs.

There is also the book from Hehre, et al. on quantum mechanical methods--
this is a self-study guide that has gotten rave reviews. 

Yvonne Martin
Abbott Laboratories
[email-masked]

*******

>From [email-masked]  Thu Jun 30 09:31:55 1994

Barry, welcome to the world of science.  I don't have a need for the home-made
program you describe because I implement full-blown modeling packages complete
with graphics in my courses (organic chemistry) for teaching purposes.  I
suspect people who teach stat. mech. may be inclined to use your stuff.  The
second question concerning  modeling programs can be found in the Appendix of a
review series I've been editing with Don Boyd called "Reviews in Computational
Chemistry" published by VCH Inc. New York.  Each volume has a complete listing
of programs, what they do and  whom to contact for more info.  Good luck,
Kenny.

************************

QCPE (Quantum Chemistry Program Exchange) is a repository for programs of this
sort.  Dr. Richard Counts at Indiana University runs it; I'm pretty sure
the address has been given on CCL in the past.  (Sorry, but I don't have it
here right now).   
Irene Newhouse

************************

Dear Barry,

Why not donate your code to the Ohio State software archive?
That way, people can evaluate it more directly and be able to 
provide an answer to your question 
"Is there any interest in using the program as a learning/teaching tool
and if so what are your requirements to make this useful?".
(especially the last part).

I am developing an advance p chem course for our chemical engineering 
seniors to take this fall as an elective, and I plan to focus on the 
use of computational methods. One of the assignments I have developed
is for the students to write their own Metropolis MC code to calculate
<U> and <U^2> for a 1D Lennard-Jones potential.  I feel that by doing
this they will gain a better understanding of the technical issues
involved in MC calculations than by using BOSS or some other "monster"
code right away. But I wasn't planning to have them develop an
MD code...so as the next assignment, I could have them do some 
calcs using your code to compare MC to MD (for 1D problems).

I will have to look at your J. Comp. Chem. article to see what your
own conclusions are, but (as one of very few people who has coded up,
run, and compared MC and MD algorithms for various properties) my own
conclusion has been that MC is the method of choice for computing 
thermodynamic (equilibrium) properties (i.e., it converges more 
rapidly w.r.t. the statistical error for a fixed number of samples
and equilibrates more rapidly)....but MD allows one to compute
time-dependent properties of the system which of course cannot be
obtained through MC.  I'd be interested to hear your perspective,
since you have obviously started from scratch and therefore are
less likely to be predjudiced by "conventional wisdom" on this point.

Best wishes and good luck in your research,

Robert Topper

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