From jkl@ccl.net  Wed Apr 19 01:31:12 1995
Received:  for jkl@ccl.net
	by www.ccl.net (8.6.10/930601.1506) id BAA17844; Wed, 19 Apr 1995 01:27:43 -0400
Date: Wed, 19 Apr 1995 01:27:43 -0400
From: Jan Labanowski <jkl@ccl.net>
Message-Id: <199504190527.BAA17844@www.ccl.net>
To: chemistry@ccl.net
Subject: Workshops at PSC
Cc: jkl@ccl.net


The following workshops at PSC have been announced:

---------------------------------------------------
                   NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS
                       WORKSHOP FOR BIOMEDICAL RESEARCHERS
                              Pittsburgh, Pennsylvania
                              June 4-9, 1995
---------------------------------------------------
                    STRUCTURE DETERMINATION FROM NMR
                    Pittsburgh Supercomputing Center
                    June 25-28, 1995
---------------------------------------------------
METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP
                    Pittsburgh Supercomputing Center
                           August 16-19, 1995
---------------------------------------------------

To find more about these (and other) workshops access the file "conferences" in
the /pub/chemistry/info directory in CCL archives. You can get there via
anon. ftp to www.ccl.net, via gopher gopher.ccl.net (port 73),
via e-mail by sending a message:
       select chemistry
       cd info
       limit 400kB
       size 60 kB
       get conferences
       quit
to MAILSERV@ccl.net

or you can get there via Web through CCL home page:
   http://www.ccl.net/chemistry.html

Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc.
Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163
ph:(614)-292-9279,  FAX:(614)-292-7168,  E-mail: jkl@ccl.net  JKL@OHSTPY.BITNET


From lrbu00@xd88.kodak.com  Wed Apr 19 10:01:19 1995
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-- 

John M. McKelvey			email: mckelvey@Kodak.COM
Computational Science Laboratory	phone: (716) 477-3335
2nd Floor, Bldg 83, RL
Eastman Kodak Company			
Rochester, NY 14650-2216

--

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	New Parameterisations in Semi-Empirical Methods
		Fall ACS Meeting, Chicago
                    August 22/23, 1995



Tuesday, 22 August

 1:40  Introductory Remarks 
J. McKelvey, Chair
Research Labs, Eastman Kodak Co., Rochester, N.Y. 14650-2216

 1:45
"Semi-Empirical Methods: An Overview"
Walter Thiel,  Organisch-chemisches Institut, Universitat Zurich, 
Winterthurerstr. 190, CH-8057 Zurich, Switzerland

 2:15
"Developing A Semiempirical Method"
J. J. P. Stewart, Stewart Computational Chemistry, 15210 Paddington Circle
Colorado Springs, CO 80921-2512

 2:45 coffee

 3:00 
"Semi-Empirical Models for Transition Metals"
W. J. Hehre Chemistry Dept., University of Ca., Irvine, Irvine, CA 92717;
Wavefunction, Inc, 18401 Von Karman Ave, Suite 370, Irvine, CA 92715 

 3:45
"Semi-Empirical Calculations of f Electron Systems"
Michael C. Zerner, Quantum Theory Project, Williamson Hall, 
University of Florida, Gainesville, FL 32611

 4:30
"Use of Semi-Empirical Methods in Direct Dynamics Calculations"
Donald Truhlar, Chemistry Department, University of Minnesotta,
Minneapolis, Minnesota 55455





Wednesday, 23 August

 9:00
"Building a Bridge Between Ab Initio and Semiempirical Theories of 
Molecular Electronic Structure"
Karl F. Freed, The James Frank Institute 
University of Chicago, Chicago, IL 60637

 9:40
"New Developments In Semi-Empirical Methods"
Walter Thiel, Organisch-chemisches Institut, Universitat Zurich, 
Winterthurerstr. 190, CH-8057 Zurich, Switzerland

10:25 coffee

10:40
"SAM1 Semi-Empirical Parameters for Transition Metals"
Andrew Holder, Chemistry Department, University Of Missouri-Kansas City,
5100 Rockhill Road, Kansas City, MO

11:20
"Parameterisation and Application of SINDO1"
Karl Jug, Theoretical Chemistry, University of Hannover, 
Am Kleinen Felde 30, D-30167 Hannover, Germany

12:05 Lunch

 1:45
"Development of an Atom-Typed NDO Scheme for NMR Predictions"
 Neil S. Ostlund, HyperCube, Inc, 419 Phillip St., Waterloo, Ontario, Canada

 2:30
"COSMO-RS: Calculation of Chemical Potentials Based on Semi-Empirical 
MO-Calculations"
Andreas Klamt, Bayer AG, D-51368 Leverkusen, Germany

 3:15 coffee

 3:30
"New Semi-Empirical Methods for Molecular Modeling in in the Condensed Phase"
Chris Cremer, Chemistry Department, University of Minnesotta,
Minneapolis, Minnesota 55455


 4:15
"Improving Numerical SCRF Techniques for Ground and Excited States"
Timothy Clark, Institut fur Organische Chemie der 
Friedrich-Alexander-Universitat Erlangen-Nurnberg, 
Henkestrasse 42, D-91054 Erlangen, Germany





 

--PART-BOUNDARY=.19504190945.ZM13943.kodak.com--



From IRIKURA@ENH.NIST.GOV  Wed Apr 19 10:16:29 1995
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From: <IRIKURA@ENH.NIST.GOV>
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 <01HPIOXBSMXS00HT7T@ENH.NIST.GOV>; Wed, 19 Apr 1995 10:03:04 EST
Date: Wed, 19 Apr 1995 10:03:04 -0500 (EST)
Subject: Force constants in redundant internal coordinates?
To: chemistry@ccl.net
Message-id: <01HPIOXBTZ5U00HT7T@ENH.NIST.GOV>
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Is there a program (or literature reference) to convert cartesian force
constants into force constants in full redundant internal coordinates? By this
I mean a force constant for every bond, every bond angle, and every torsion,
for a total in excess of 3N-6.  The results are of interest to one of the
spectroscopists here at NIST, and he wants to avoid re-inventing the wheel. 
I believe the stretches are of special interest.

Any help will be appreciated!

Karl Irikura

----------------------------------------------
Dr. Karl Irikura
Chemical Kinetics and Thermodynamics Division
National Institute of Standards and Technology
Gaithersburg, MD  20899
----------------------------------------------

From mfrancl@cc.brynmawr.edu  Wed Apr 19 13:01:24 1995
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From: <mfrancl@cc.brynmawr.edu>
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Date: Wed, 19 Apr 1995 12:54:46 -0400
Message-Id: <9504191654.AA10298@cc.brynmawr.edu>
To: chemistry@ccl.net
Subject: bug in G92 calculation of corrections for enthalpies


Has anyone else noticed that G92 doesn't correct calculate the H-H(0)
corrections (the thermal energies)?  They can be off by as much as a factor
of 10!  The problem appears to be in the calculation of the vibrational
contribution.  Since we can duplicate the JANAF data, I assume we are doing
the calculation correctly.  

Michelle M. Francl
Associate Professor of Chemistry
Bryn Mawr College
Bryn Mawr, PA 19010

Phone:  610-526-5108
FAX:  610-526-5086
Internet: mfrancl@cc.brynmawr.edu


From m10!frisch@uunet.uu.net  Wed Apr 19 15:31:23 1995
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Date: Wed, 19 Apr 95 15:01:40 EDT
From: m10!frisch@uunet.uu.net (Michael Frisch)
Subject: Re: CCL:bug in G92 calculation of corrections for enthalpies
To: chemistry@ccl.net
In-Reply-To: <uunet!cc.brynmawr.edu!mfrancl>, Wed, 19 Apr 1995 12:54:46 -0400


    Has anyone else noticed that G92 doesn't correct calculate the H-H(0)
    corrections (the thermal energies)?  They can be off by as much as a factor
    of 10!  The problem appears to be in the calculation of the vibrational
    contribution.  Since we can duplicate the JANAF data, I assume we are doing
    the calculation correctly.  
    
We've certainly checked these by hand.  There are different conventions for
different purposes, so perhaps you could be more specific about what you're
doing and what you expect the program is doing.

Mike Frisch
-------

From mfrancl@cc.brynmawr.edu  Wed Apr 19 16:31:24 1995
Received: from cc.brynmawr.edu  for mfrancl@cc.brynmawr.edu
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From: <mfrancl@cc.brynmawr.edu>
Received: by cc.brynmawr.edu (5.65/DEC-Ultrix/4.4)
	id AA23673; Wed, 19 Apr 1995 16:21:24 -0400
Date: Wed, 19 Apr 1995 16:21:24 -0400
Message-Id: <9504192021.AA23673@cc.brynmawr.edu>
To: chemistry@ccl.net
Subject: G92 corrections to the enthalpy


The solution to the mystery of the irreproducible numbers in G92:

The key is in a footnote on pg. 115 of Foresman and Frisch "Exploring
Chemistry with Electronic Structure Methods" where it says that the zero
point energy is
folded into the vibrational part of the H-H(0).  I was assuming that the
corrections listed in the G92 output table under the heading "thermal
energies"were the H-H(0) corrections (they are for the translational and
rotational parts) and was adding in the  zero point energy separately. 
Since the G92 documentation refers you to the equations in McQuarrie --
where ZPE is NOT considered part of the thermal energy, but an entirely
separate correction term -- my assumption seemed reasonable.  Mystery
solved - thanks to all who responded!


Michelle M. Francl
Associate Professor of Chemistry
Bryn Mawr College
Bryn Mawr, PA 19010

Phone:  610-526-5108
FAX:  610-526-5086
Internet: mfrancl@cc.brynmawr.edu


From ar1z+@andrew.cmu.edu  Wed Apr 19 17:01:25 1995
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From: "Alexander J. Ropelewski" <ar1z+@andrew.cmu.edu>
To: Outbound News
    <outnews+netnews.news.announce.conferences@andrew.cmu.edu>
Subject: CCL:STRUCTURE DETERMINATION FROM NMR
Cc: Outbound News <outnews+netnews.bionet.announce@andrew.cmu.edu>,
        Outbound News <outnews+netnews.sci.research@andrew.cmu.edu>,
        Outbound News
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        Outbound News
    <outnews+netnews.bionet.molec-model@andrew.cmu.edu>,
        Outbound News
    <outnews+netnews.bionet.molbio.proteins@andrew.cmu.edu>,
        Outbound News <outnews+netnews.bionet.cellbiol@andrew.cmu.edu>,
        Outbound News <outnews+netnews.sci.research@andrew.cmu.edu>,
        Outbound News
    <outnews+netnews.sci.techniques.spectroscopy@andrew.cmu.edu>,
        Outbound News
    <outnews+netnews.sci.bio.technology@andrew.cmu.edu>,
        rna@net.bio.net, chemistry@ccl.net,
        Outbound News
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        str-nmr@net.bio.net, bruker-users-mail@bloch.cchem.berkeley.edu,
        ammrl-request@bloch.cchem.berkeley.edu


                    STRUCTURE DETERMINATION FROM NMR
                    Pittsburgh Supercomputing Center
                    June 25-28, 1995


Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a
"Structure Determination From NMR" Workshop.  The objective is to introduce
participants to the different techniques for the elucidation of solution
structures of biological macromolecules from nuclear magnetic resonance data.
The workshop is free to academic participants.


The worskhop will consist of lectures and extensive hands-on sessions.
The programs AMBER, Mardigras and MidasPlus will be discussed.  Hands-on
sessions will be emphasized.
Participants will be able to work on the examples
provided or on their own experimental data.
No prior supercomputing experience is necessary.

Workshop leaders are: Dr. David Case, The Scripps Research Institute; and
Drs Thomas James, Julie Newdoll and Uli Schmitz,
University of California, San Francisco.

This workshop is funded by a grant from the Biomedical Research Technology
Program, National Center for Research Resources, National Institutes of
Health. TRAVEL, MEALS AND HOTEL ACCOMMODATIONS FOR RESEARCHERS AFFILIATED
WITH U.S. ACADEMIC INSTITUTIONS ARE SUPPORTED BY THIS GRANT.
Enrollment is limited to 20.  An application form is included.
Deadline for applications is April 28, 1995.

Additional information about this workshop can be found in
http://pscinfo.psc.edu/biomed/workshops95.html




                             * * * * * * * * * *



                             PITTSBURGH SUPERCOMPUTING CENTER
                             BIOMEDICAL  INITIATIVE
                             STRUCTURE DETERMINATION FROM NMR
                             June 25-28, 1995

                             APPLICATION


Name:________________________________________________________________________

Affiliation:_________________________________________________________________

Address:_____________________________________________________________________
                                  (Business)
_____________________________________________________________________________

____________________________________________________________________________
                                    (Home)
____________________________________________________________________________

Telephone:  ____________________              ______________________
                (Business)                            (Home)

*Social Security Number:  _______-_____-_______    Citizenship: ____________

Electronic Mail Address:____________________________________________________

Status: ___Graduate  ___Post-doctoral Fellow  ___Faculty  ___Other (specify)

Please indicate specifically any special housing, transportation or dietary
arrangements you will need:  _______________________________________________

How did you learn about this workshop? _____________________________________


REQUIREMENTS:

Applicants must submit a completed application form and a cover letter. The
letter should describe, in one or two paragraphs, your current research and
how participating in the workshop will enhance this research.  Please
include a brief statement describing your level of experience with computers.
Faculty members, staff and post-docs should provide a curriculum vita.
Graduate students must have a letter of recommendation from a faculty member.

Please return all application materials by APRIL 28, 1995 to:

          Biomedical Workshop Applications Committee
          Pittsburgh Supercomputing Center
          4400 Fifth Avenue, Suite 230C
          Pittsburgh, PA 15213

Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960.

*Disclosure of Social Security Number is voluntary.

PSC does not discriminate on the basis of race, color, religion, sex, age,
creed, national or ethnic origin, or handicap.


From ar1z+@andrew.cmu.edu  Wed Apr 19 17:01:28 1995
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Date: Wed, 19 Apr 1995 16:49:08 -0400 (EDT)
From: "Alexander J. Ropelewski" <ar1z+@andrew.cmu.edu>
To: Outbound News
    <outnews+netnews.news.announce.conferences@andrew.cmu.edu>
Subject: CCL:Methods of Molecular Mechanics and Dynamics of Biopolymers workshop
Cc: Outbound News <outnews+netnews.bionet.announce@andrew.cmu.edu>,
        Outbound News <outnews+netnews.sci.research@andrew.cmu.edu>,
        Outbound News
    <outnews+netnews.sci.techniques.mag-resonance@andrew.cmu.edu>,
        Outbound News
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        Outbound News
    <outnews+netnews.bionet.molbio.proteins@andrew.cmu.edu>,
        Outbound News <outnews+netnews.bionet.cellbiol@andrew.cmu.edu>,
        Outbound News <outnews+netnews.sci.research@andrew.cmu.edu>,
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        Outbound News
    <outnews+netnews.sci.bio.technology@andrew.cmu.edu>,
        rna@net.bio.net, chemistry@ccl.net


"METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP
                    Pittsburgh Supercomputing Center
                           August 16-19, 1995


The Pittsburgh Supercomputing Center (PSC) is hosting a workshop
on "Methods of Molecular Mechanics and Dynamics of Biopolymers,"
August 16-19, 1995.
The workshop will familiarize biomedical researchers with
computational methods and provide practice
in applying supercomputing resources to problems of concern in molecular
mechanics.  Practical experience on our supercomputers will be gained in
the application to:
(1) the theory and practice of molecular mechanics and dynamics;
(2) the development and refinement of molecular mechanics force fields;
(3) the problem of conformation mapping and analysis of polypeptide
structures, including the refinement of structure from measured NMR data;
and
(4) computation of interaction energies and free energies for protein-drug
interactions and conformational thermodynamics.

Workshop leaders are
Dr. Charles L. Brooks III, The Scripps Research Institute
and
Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore.

The worskhop will consist of lectures and extensive hands-on sessions.
General aspects of molecular mechanics software will be discussed and
a number of packages are available for use at the PSC.  However,
the programs CHARMM and QUANTA will be utilized most extensively in
demonstrations.  Hands-on sessions will be emphasized.
Participants will be able to work on the examples provided or
on their own experimental data.
No prior supercomputing experience is necessary.

This workshop is funded by a grant from the Biomedical Research Technology
Program, National Center for Research Resources, National Institutes of
Health.  TRAVEL, MEALS AND HOTEL ACCOMMODATIONS FOR RESEARCHERS AFFILIATED
WITH U.S. ACADEMIC INSTITUTIONS ARE SUPPORTED BY THIS GRANT.
Enrollment is limited to 20.  An application form is included.
Deadline for applications is: June 22, 1995.
Please direct inquires or send the following application form to
blankens@psc.edu.

Additional information about this workshop can be found in
http://pscinfo.psc.edu/biomed/workshops95.html



                         PITTSBURGH SUPERCOMPUTING CENTER
                         BIOMEDICAL  INITIATIVE
                         **************************************
                         August 16-19, 1995

                         APPLICATION


Name:________________________________________________________________________

Affiliation:_________________________________________________________________

Address:_____________________________________________________________________
                                  (Business)
_____________________________________________________________________________

____________________________________________________________________________
                                    (Home)
____________________________________________________________________________

Telephone:  ____________________              ______________________
                (Business)                            (Home)

*Social Security Number:  _______-_____-_______    Citizenship: ____________

Electronic Mail Address:____________________________________________________

Status: ___Graduate  ___Post-doctoral Fellow  ___Faculty  ___Other (specify)

Please indicate specifically any special housing, transportation or dietary
arrangements you will need:  _______________________________________________

How did you learn about this workshop? _____________________________________


REQUIREMENTS:

Applicants must submit a completed application form and a cover letter. The
letter should describe, in one or two paragraphs, your current research and
how participating in the workshop will enhance this research.  Please
include a brief statement describing your level of experience with computers.
Faculty members, staff and post-docs should provide a curriculum vita.
Graduate students must have a letter of recommendation from a faculty member.

Please return all application materials by June 22, 1995 to:

          Biomedical Workshop Applications Committee
          Pittsburgh Supercomputing Center
          4400 Fifth Avenue, Suite 230C
          Pittsburgh, PA 15213

Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960.

*Disclosure of Social Security Number is voluntary.

PSC does not discriminate on the basis of race, color, religion, sex, age,
creed, national or ethnic origin, or handicap.



From m10!frisch@uunet.uu.net  Wed Apr 19 18:01:25 1995
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Received: by m10.gaussian.com; Wed, 19 Apr 95 17:47:06 EDT
Date: Wed, 19 Apr 95 17:47:06 EDT
From: m10!frisch@uunet.uu.net (Michael Frisch)
Subject: G92 calculation of corrections for enthalpies
To: chemistry@ccl.net
In-Reply-To: Steen Hammerum <uunet!kiku.dk!steen>, Wed, 19 Apr 1995 22:44:03 +0200 (METDST)


    >     Has anyone else noticed that G92 doesn't correct calculate the H-H(0)
    >     corrections (the thermal energies)?  They can be off by as much as a factor
    >     of 10!  The problem appears to be in the calculation of the vibrational
    >     contribution.  Since we can duplicate the JANAF data, I assume we are doing
    >     the calculation correctly.  
    >     
    > We've certainly checked these by hand.  There are different conventions for
    > different purposes, so perhaps you could be more specific about what you're
    > doing and what you expect the program is doing.
    > 
    > Mike Frisch
    
Someone asked me to be more specific.  Gaussian 92 produces thermal
corrections which include vibrational energy in the harmonic approximation,
(i.e., assuming a Boltzman distribution of vibrational states using the
expressions from standard stat mech texts, such as McQuarrie's book),
rotational energies assuming a rigid rotor (i.e., 3/2 kT) and translational
energies (also 3/2 kT).

Since most of the vibrational energy is zero-point energy, which is
trivially verified, I don't see how this term or the overall thermal energy
could be off by an order of magnitude.

Partition functions are computed relative to both the bottom of the
vibrational well and with respect to the lowest vibrational state.  Which of
these to use depends on whether your convention is to include the zero point
terms in the activation barrier for a reaction or in the pre-factor when
computing a reaction rate.  Heat capacities also reported and are computed
using expressions from McQuarrie's book.  Neither of these quantities is
relevent to computing reaction energies, enthalpies, or free energies.

The original question referred to energies but also uses the expression
H-H(0), so I don't know if the question refers to energies or enthalpies.
Just in case, I'll comment on computing enthalpies.

Gaussian 92 doesn't compute enthalpies at all.  To convert the energy at
a finite temperature to an enthalpy, one needs to know the Delta(PV) between
the system and it's standard state.  In practice, the easy thing to do is
to compute a Delta-E for a reaction and then convert to a Delta-H of reaction
by assuming an ideal gas and correcting by RT * Delta(N) (change in number of
molecules in the reaction).

Gaussian 94 does report an enthalpy, which is the energy at the requested
temperature plus RT.  This is not a Delta-H with respect to a standard state,
but can be used to compute a Delta-H for a reaction by simply taking the
algebraic sum of the enthalpies printed by the program for reactants and
products, in which case the extra RT terms just automatically sum up to the
RT * Delta(N) correction above.

That's as much as I can say without knowing more specifically what the
discrepancy in the orginal posting referrs to.

Mike Frisch
frisch@lorentzian.com
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