From bhardy@helix.nih.gov  Tue Jul 12 01:52:35 1994
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Date: Tue, 12 Jul 94 00:56:00 -0400
From: bhardy@helix.nih.gov (Barry J. Hardy)
Message-Id: <9407120456.AA23398@helix.nih.gov>
To: chemistry@ccl.net
Subject:  Response to request for learning programs


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
MartinY@Abbott.com

*******


From lipkowitz@chem.iupui.edu  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

************************************************************************
 Prof. Robert Q. Topper               internet:   topper@cooper.edu
 Department of Chemistry              phone:      (212) 353-4378
 The Cooper Union                     FAX:        (212) 353-4341 
 Cooper Square                        subway:     take the N/R to 8th/NYU 
 New York, NY 10003 USA                           or the 6 to Astor Place

 The Cooper Union for the Advancement of Science and Art, established 
 by Peter Cooper in 1859, is a private institution of higher learning 
 where all students receive full-tuition scholarships.                 
************************************************************************



From SB@CHEM.UNI.WROC.PL  Tue Jul 12 08:52:42 1994
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From: "Slawomir Berski" <SB@CHEM.UNI.WROC.PL>
To: chemistry@ccl.net
Date:          Tue, 12 Jul 1994 13:55:57 GMT+1
Subject:       PM3,AM1 - radicals
Priority: normal
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Hi,
I'm interested in comparison of experimental and calculated
 by PM3 and AM1 methods heats of formation of different radicals.
 Do you know any references on this topic ?
 
 Thanks !
 
                                 Slawek

From DAREK@ichn.ch.pwr.wroc.pl  Tue Jul 12 08:54:56 1994
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From: "Dariusz C.Bienko" <DAREK@ichn.ch.pwr.wroc.pl>
Organization:  Inst. of Inorg. Chem. PWr.
To: chemistry@ccl.net
Date:          Tue, 12 Jul 1994 14:13:51 GMT+100
Subject:       guestion about program
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Czesc,
I search for the program to count the potential energy distribution 
from Gaussian 92(90) output.
I'd like it to count the percentage contribution of internal 
coordinate in the normal mode.
                                                Darek

From suter@physik.unizh.ch  Tue Jul 12 09:53:10 1994
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From: Hans-Ueli Suter <suter@physik.unizh.ch>
Message-Id:  <9407121306.AA09273@milliways.physik.unizh.ch>
Subject: AO based DFT codes
To: chemistry@ccl.net
Date: Tue, 12 Jul 1994 15:05:58 +0200 (MET DST)
Cc: suter@ccl.net (Hans-Ueli Suter)
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Dear Netters,

I would be very happy to hear something about the current 
use and the experiences of some AO based  desity functional
codes. As far as I see this includes the programs
DMol (Delley), G92/DFT (Pople), DeFT and DeMon and
ADF.  For these there are the following two questions:

(i) Is this list complete, which program should be addeed?

(ii) What program are you using, what is your experience
      with it. how fast, how userfriendly and how stable
     is your program?

I will try to summarize the answers and submit them to the
net, if requested.

                            sorry, for wasting your time,

                              Hans Ulrich  Suter
                              CSCS, Manno, Switzerland.


From gene@jersey.cray.com  Tue Jul 12 13:52:49 1994
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From: gene@jersey.cray.com (Eugene Fleischmann)
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To: suter@physik.unizh.ch
Cc: chemistry@ccl.net, gene@jersey.cray.com, george@gravity.cray.com,
        raeuchle@gravity.cray.com
Subject: Re: CCL:AO based DFT codes
Content-Length: 3622


> From chemistry-request@ccl.net Tue Jul 12 12:04 EDT 1994
> Subject: CCL:AO based DFT codes
> To: chemistry@ccl.net
> Cc: suter@ccl.net (Hans-Ueli Suter)
> 
> Dear Netters,
> 
> I would be very happy to hear something about the current 
> use and the experiences of some AO based  desity functional
> codes. As far as I see this includes the programs
> DMol (Delley), G92/DFT (Pople), DeFT and DeMon and
> ADF.  For these there are the following two questions:
> 
> (i) Is this list complete, which program should be addeed?
> 
> (ii) What program are you using, what is your experience
>       with it. how fast, how userfriendly and how stable
>      is your program?
> 
> I will try to summarize the answers and submit them to the
> net, if requested.
> 
>                             sorry, for wasting your time,
> 
>                               Hans Ulrich  Suter
>                               CSCS, Manno, Switzerland.
> 

Greetings, Prof. Suter.  With regard to your inquiry:

> (i) Is this list complete, which program should be addeed?

The only addition to your list is:  DGauss, from Cray Research, Inc.


> (ii) What program are you using, what is your experience
>      with it. how fast, how user-friendly and how stable
>      is your program?

I use DGauss regularly, for obvious reasons.  It is a VERY user-friendly
DFT program as a stand-alone code, and even MORE user-friendly when used
with the GUI for Silicon Graphics known as:  UniChem.  DGauss is VERY
fast on Cray vector hardware, and it is also fast on SGI workstations.

The program uses gaussian functions, in the spirit of standard "ab initio"
programs today, to build the density and solve the Kohn-Sham equations.
In its present implementation, DGauss uses an all-electron non-relativistic
Hamiltonian.  The major functions of DGauss include geometry optimizations
for stationary points (minima and saddle points) on a potential energy
hypersurface.  These optimizations are carried out using analytical first 
derivatives.  Until the next release, vibrational frequencies as well as
infrared intensities are computed with finite difference techniques.  For
fixed or optimized geometries, DGauss evaluates molecular properties such 
as Mulliken charges, multipole moments, molecular orbitals, electron densities,
spin densities, and electrostatic potentials.  At present, SCF calculations 
can be carried out on the local spin density (LSD) functional level, or at 
the non-local (NLSD) level using Becke-Perdew or Becke-Stoll-Preuss-Pavlidou 
gradient corrections after the SCF or Becke-Perdew or Becke-Lee-Yang-Parr 
corrections self-consistently.  DGauss calculates molecular orbitals (MOs) 
and the corresponding orbital energies.  It is designed to take full advantage 
of the current knowledge of vector and parallel algorithms in the evaluation 
of integrals and other computationally demanding numerical procedures, such as 
the calculation of the exchange-correlation terms which are calculated 
numerically on a finite grid.

For more information about DGauss and/or UniChem please send mail to any of
the following individuals at Cray Research, Inc:

Dr. George Fitzgerald        george@gravity.cray.com
Dr. Thomas Raeuchle          raeuchle@gravity.cray.com
Dr. Eugene Fleischmann       gene@jersey.cray.com

Best Wishes,

Gene

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
	Eugene D. Fleischmann, Ph.D.
	Computational Chemist
	Cray Research, Inc.		(609) 252-1250
	121 Commons Way			gene@jersey.cray.com
	Princeton, NJ  08540
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

From kevin@chem.ucla.edu  Tue Jul 12 14:52:51 1994
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Date: Tue, 12 Jul 94 11:13:02 -0700
From: kevin@chem.ucla.edu (Kevin Condroski)
Message-Id: <9407121813.AA25956@houksg1.chem.ucla.edu>
To: chemistry@ccl.net
Subject: Basis Sets for Trasition Metals (Mn)



	Fellow theoreticians:

	I am pursuing an ab initio study of Mn complexes, and I have learned 
the hard way that small basis sets (i.e., STO-3G*, and Hehre's 3-21G extension
for transition metals) are woefully inadequate for such calculations due to
convergence difficulties and downright inaccurate results (to put it bluntly).

	I have found several references to more extensive basis sets from the
literature; however, most of these are atomic sets without polarization 
functions included that have been optimized for molecular calculations.  Again,
these are quite inaccurate without polarization functions.

	If anyone has any leads to a collection of basis sets that are optimized
for molecular calculations (online or otherwise), I would greatly appreciate
your input.  Any suggestions for polarization functions to add to the better
atomic basis sets are also welcome.  Thanks for your help!


					Kevin Condroski
					(PostDoc, UCLA)

					kevin@houksg1.chem.ucla.edu



From billg@SCGROUP.BARRNET.NET  Tue Jul 12 15:00:00 1994
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From: billg@scg.fujitsu.com (Marketing)
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To: chemistry@ccl.net
Subject: environ. model summary


Dear Netters,

Here is the summary of responses to my query regarding environmental
modeling, which were extremely helpful. I have since obtained
two of the codes (PRZM and GLEAMS) from the EPA and USDA offices
listed in the postings below.

Many thanks again to all who responded or expressed interest.


Bill Glauser 

---------------------------------------------------------------------------

(Original posting)

 |Has anyone heard of any of the following codes:
 |  PRZM, GLEAMS, EXAMS, and EPIC

 |They are presumably used for environmental modeling to
 |assess the fate of pollutants in the environment.

 |I am curious as to the models that underlie these codes.
 |For example, what kinetic, thermodynamic, and transport
 |models are used to determine how a compound partitions
 |between the water, ground, and atmosphere?

 |On a related note, what is the level of maturity of the field
 |of environmental modeling (probably macroscopic)
 |versus molecular modeling (microscopic)?

 |Finally, where can one obtain these codes and on which platforms
 |do they run?

 |Thanks in advance for your help.


 |Bill

---------------------------------------------------------------------------
From: bowlus@palres.dnet.sandoz.com (Steve Bowlus)

GLEAMS and PRZM (and possibly the others) are soil fate models, commonly 
used in the pesticide industry for modeling runoff of pesticides from 
fields.  I forget the exact acronyms, but they are something like _G_round 
_L_oading _E_ffect... and _P_esticide _R_oot _Z_one _M_odel. . .you can get 
the drift from the names.  These are transport models, which depend on the 
physical properties of the materials being modeled.  At this point, the 
only "molecular modeling" that I have done in the systems is to evaluate 
physical properties, such as partition coefficients and Henry's constants.

Try R.A. Leonard, W.G. Kinsel and D.A. Still, Transac. Am. Soc. Ag. 
Engineers, vol 30 no. 5 (1987) for a description of GLEAMS.  

You can get a lot more information about these models from our biologists 
at our Gilroy test center:  talk to Rakesh Jain or Bob Lamoreaux.  We use a 
program called PRE-AP, which is a front end for GLEAMS.  Their number is (
408) 848-1474.

sb

---------------------------------------------------------------------------

From: Dr. Dave Winkler <D.Winkler@chem.csiro.au>


I would greatly appreciate a summary of the responses.


---------------------------------------------------------------------------

From: jim@ni-ait.co.jp (CGI Jim Jones)

Bill,

My company consults on high-level nuclear waste disposal and we are familiar    with most codes related to the environment, but have not heard the four that youmention.

There are several places you might try:

Energy Science and Technology Software Center
	e-mail:	ESTSC@ADONIS.OSTL.GOV

	phone:	703-487-4753

Let me know if you don't get what you want from those and I'll see if I can
point you to some other places.

If you do find out any information on those applications, could you let me know?


--------------------------------------------------------------------------

From: gmeier@ncsa.uiuc.edu (Gary Meier)

I've had very limited exposure to PRZM (Pesticide Root Zone Model) and
GLEAMS (Groundwater Loading Effects of Agricultural Management Systems).
The former is available from the U. S. Environmental Protection Agency
Center for Exposure Assessment Modeling (CEAM) in Athens, Georgia,
(706)-546-3549.  The latter is available from the U. S. Department of
Agriculture, Agricultural Research Service.  Contact J. R. Williams or C.
W. Richardson at the Grassland, Soil & Water Research Lab in Temple, Texas,
817-770-6500.  As of a year ago, both programs were available without
charge (I think they want you to send them blank disks).  I believe both
programs run only on IBM PCs and clones.

I don't know a lot about the models that underly the codes, but PRZM at
least permits very detailed modeling of pesticide movement in the surface
water, throught the root zone, and in the ground water.  Effects of
weather, soil and crop types (including crop rotation), irrigation (if
used), pesticide application rate and timing, and a host of other
parameters are entered.  Pesticide movement is calculated using daily time
steps in simulations that typically cover several years to several decades.
When I was playing with the program, a three-year simulation of low to
moderate complexity required just 3 or 4 minutes on a 25 mhz 486 PC.

I haven't had opportunity to validate the programs or do any other
comparisons to real-world results, so I can't comment on how accurate the
simulations are.

I hope you find this useful.

Gary

--------------------------------------------------------------------------

From shawn@wucmd.wustl.edu Thu Jul  7 08:04:17 1994

Please summarize your responses for this interesting question for the net.
Thank You.

Shawn Huston


--------------------------------------------------------------------------


From: gerson@VNET.IBM.COM (Dennis J. Gerson, Ph.D.)

Bill, all the codes you mentioned are used in groundwater or underground
reservoir modeling.  The codes do have chemical knowledge thru group
function activity coefficients and fugacities (ala Aspen).  The major
users of these codes are the oil companies and environmental remediation
companies.  The codes all run on SGI with OpenGL, IBM RISC with OpenGL
they may support Uniras Unigraphics, thus SUN, DEC, HP and IBM.

Regards, Dennis Gerson

--------------------------------------------------------------------------

From: slee@theochem.uwaterloo.ca (Tom Slee)

Hi Bill,

I don't know any of the codes you mention.  However, my impression is
that most environmental models work on a cell basis.  You set up your
system as a set of cells: one cell may be a lake, one the atmosphere,
one the ground nearby, one the fish within the water, etc.  (I don't 
know how coarse or fine these
cells can be now).  Then you set up differential equations describing
the flow of materials of interest from one cell to another (or to
nowhere in the case of degradation).  These equations may be transport
equations, or may represent chemical processes: generally you will have
both physical and chemical processes affecting the distribution.  Then 
you solve your system of equations numerically.

There are clearly lots of approximations in this kind of model: it is
implicit that there is perfect mixing within each cell, and the
equations dramatically simplify the factors in determining the
distribution.  There are also, however, lots of empirical numbers 
that need to be known and typically are not.  The rate of mixing of one
"cell" with another must be very dependent on site, and many other
rates are not well known, so in the end you have a very empirical
model. 

This about sums up my total knowledge of the subject, so don't ask any
questions!

		Tom

From rob@retina.chem.psu.edu  Tue Jul 12 17:52:48 1994
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From: rob@retina.chem.psu.edu (Rob Stanton)
Message-Id: <9407122114.AA21889@retina.chem.psu.edu>
To: CHEMISTRY@ccl.net
Subject: vdw params for Cd and Hg


Has anyone developed or know of any published vdW parameters for Cd or Hg???
Please respond directly to me and thanks for any help.

                                       Rob

____________________________________________________________________________
   *    *       *      
*            *      * *                  Robert V. Stanton
      *    *     *                             
*  *    *     *     *                    tel   814-863-7591
 *    * /\ */\   *                       email rob@retina.chem.psu.edu
   /\  /--\/__\  /\   *                  152 Davey Lab
* /--\/    \   \/--\                     Penn State University
 /   /      \  /    \                    Univ. Park, PA 16802
/   /        \/      \                   USA
Go Climb a mountain!!!!
_____________________________________________________________________________


From ghislain@unb.ca  Tue Jul 12 20:52:48 1994
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To: CHEMISTRY@ccl.net
From: ghislain@unb.ca (Ghislain Deslongchamps)
Subject: MM parameters for enolized beta-ketoester


Dear CCl'ers

Does anyone know where I can find MM2 or AMBER parameters for enolized
beta-ketoesters?  I need to model a series of compounds containing an
enolized 2-carbomethoxycyclopentanone.

Thanks

Ghis


+++++++++++++++++++++++++++++++++++++++++++++++++++++
+    Ghislain Deslongchamps,  Assistant Professor   +
+    Department of Chemistry                        +
+    University of New Brunswick                    +
+    Fredericton, N.B.  CANADA  E3B 5A3             +
+    e-mail:  GHISLAIN@UNB.CA                       +
+    phone:   506-453-4795 (or 453-4792)            +
+    FAX:     506-453-4599                          +
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