From JSMCM@jazz.ucc.uno.edu  Thu Dec  1 04:16:17 1994
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Date: 01 Dec 1994 03:14:27 -0600 (CST)
From: JORGE <JSMCM@jazz.ucc.uno.edu>
Subject: Liquid Nitromethane
To: chemistry@ccl.net
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Dear CCL members,
I am looking for information on liquid nitromethane.
I would appreciate if you could send me any information
related to the theoretical study of this liquid. This is
to complement a combined study DFT/MD that we are running.
I will be glad to summarize the results to the net if there
is some interest. Thanks in advance.
With my best regards

Jorge M. Seminario
Department of Chemistry
University of New Orleans
New Orleans, LA 70148
Phone 504-286-7216
FAX   504-286-6860
jsmcm@uno.edu

From Patrick.Bultinck@rug.ac.be  Thu Dec  1 04:33:00 1994
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Date: Thu, 1 Dec 1994 09:54:04 +0100 (MET)
From: Patrick Bultinck <Patrick.Bultinck@rug.ac.be>
To: "comp. chem. list" <chemistry@ccl.net>
Subject: RMS deviation in El.stat. pot. (GAMESS)
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Dear netters,

I have a question on some GAMESS (maybe other programs too) output 
generated in the fit of charges to the electrostatic potential.
The output is given underneath. It describes a fit of charges on the 
atoms in an ethylenediamine conformer. As constraints we've used :
1- the sum of charges must equal the total charge (zero)
2- fit must reproduce dipole moment
3- fit must reproduce the quadrupole moment

The algorithm used is the connolly algorithm.

Can somebody tell me what the RMS deviation (in units kcal/mole) means, 
and how do they calculate it ? On what scale do I have to view the values ?

OUTPUT

          -----------------------
          ELECTROSTATIC POTENTIAL
          -----------------------

     NUMBER OF POINTS SELECTED FOR FITTING =  1418

 NET CHARGES:
 ---------------------------
 ATOM                CHARGE
 ---------------------------
 C1                  1.7740
 C2                  1.7740
 N1                 -1.2473
 N2                 -1.2473
 H1                  0.2977
 H2                  0.2977
 H3                  0.2977
 H4                  0.2977
 H5                 -0.5611
 H6                 -0.5611
 H7                 -0.5611
 H8                 -0.5611
 ---------------------------

******Here it is******
 RMS DEVIATION IS            3.390 KCAL/MOLE
 RELATIVE RMS DEVIATION IS  38.589 %
***********************

 MULTIPOLE MOMENTS:
 ---------------------------------------------------------
 STATUS  ACTUAL VALUE       QUANTITY        FITTED VALUE 
 ---------------------------------------------------------
 FIXED       0.0000       TOTAL CHARGE       0.0000
             0.0000 D    DIPOLE MOMENT       0.0000 D
 FIXED       0.0000 D          DX            0.0000 D
 FIXED       0.0000 D          DY            0.0000 D
 FIXED       0.0000 D          DZ            0.0000 D
 FREE       -9.7610 BU         QXX          -9.7610 BU
 FIXED       2.3702 BU         QYY           2.3702 BU
 FIXED       7.3908 BU         QZZ           7.3908 BU
 FIXED     -10.5572 BU         QXY         -10.5572 BU
 FIXED       0.0000 BU         QXZ           0.0000 BU
 FIXED       0.0000 BU         QYZ           0.0000 BU
 ---------------------------------------------------------

From rull@RHINO.chem.ruu.nl  Thu Dec  1 05:16:17 1994
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From: rull@RHINO.chem.ruu.nl (Ton Rullmann)
Message-Id: <9412011036.AA18486@RHINO>
Subject: awk to C conversion
To: chemistry@ccl.net
Date: Thu, 1 Dec 1994 10:36:17 +0000 (WET)
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Hello,
I am looking for a program to convert a (n)awk script into a C program.
At least one such utility appears to exist: awkcc, but I don't know where
to obtain it.
Can anyone give me references to awkcc or similar programs (how to obtain,
commercial or PD)?
Thank you!
-- 
| Ton Rullmann                                NMR Spectroscopy            |
| Bijvoet Center for Biomolecular Research  | Tel. : int+31.30.533641     |
| Utrecht University, Padualaan 8,          | Fax  : int+31.30.537623     |
| 3584 CH Utrecht, The Netherlands          | Email: rull@nmr.chem.ruu.nl |


From JeanLuc.Verschelde@rug.ac.be  Thu Dec  1 06:16:18 1994
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Date: Thu, 1 Dec 1994 11:36:38 +0100 (MET)
From: Jean-Luc Verschelde <JeanLuc.Verschelde@rug.ac.be>
To: OHIO SUPER <CHEMISTRY@ccl.net>
Subject: large scale movements
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Hi all,

	I want to simulate the large scale movements of the lid
	on horse pancreatic lipase . Therefore I need a brownian
	dynamics algorithm .
	Where can I find this algorithm and do you agree that this
	algorithm is the best for this problem?

		Thanks,	

			Jean-Luc


From bgobbi@CHBS.CIBA.COM  Thu Dec  1 07:16:21 1994
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From: "Alberto Gobbi" <bgobbi@CHBS.CIBA.COM>
To: CHEMISTRY@ccl.net
Date:          Thu, 1 Dec 1994 12:52:57 +1
Subject:       Available Chemical Databases 2
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Priority: normal
X-Mailer: Pegasus Mail/Windows (v1.22)


I yust have got this mail today from MDL,
Alberto

------- Forwarded Message Follows -------
From:          DM@mdli.com

DATABASE PRODUCTS FROM MDL INFORMATION SYSTEMS

1-800-635-0064

14600 Catalina Street
San Leandro, CA  94577
contact cherylk@mdli.com


PHARMACEUTICAL DATABASES

MDL Drug Data Report (MDDR)

The MDDR database contains structure and biological activity 
information for 57,000 drug candidates.  Every month it is updated 
with new biologically active compounds as they are disclosed.  The 
progress of these compounds are then tracked through development 
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valuable in helping to identify structural features which may contribute 
to a given biological activity and in staying abreast of competitive 
discoveries.  A 3D version is available.

Comprehensive Medicinal Chemistry-3D (CMC-3D)

The CMC-3D database provides 3D models and important biochemical 
properties for 6,500 compounds with biological activity.  Developed 
>from Pergammon s Comprehensive Medicinal Chemistry, data include
synonyms, drug class, log P, and pKa.


DATABASES OF AVAILABLE CHEMICALS

The Available Chemicals Directory (ACD)

The Available Chemicals Directory provides chemists with an efficient 
way to find supplier and pricing information for both research-grade 
and bulk chemicals.  ACD includes 171,000 chemical substances 
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Chemical Products Information (CPI) file

The CPI file consists of supplier and pricing information for 418,000 
chemical products built into preconfigured relational tables in ASCII 
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Ingress, and Rdb.  The CPI file has an annual right-to-use license and 
can only be purchased if ACD has been licensed.

Custom Databases for High-throughput Screening

With the inclusion in ACD of large libraries of compounds that can be 
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OHS MSDS on Disc

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OHS MSDS Reference Database

The OHS MSDS Reference Database has 48,000 MSDS for 16,000 
pure substances and 32,000 mixtures.  It is updated quarterly and is 
used by the customers of chemical companies to provide their 
employees immediate access to safety label information, summary 
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user interfaces.

OHS MSDS Inventory Match Database

This file of 90,000 independently-researched MSDS is used to match all 
entities in a company s chemical inventory system and is updated 
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provide 100% coverage.  This database is used as both a research 
reference tool and for regulatory compliance.  A right-to-distribute 
license for individual MSDS is also available to chemical 
manufacturers.


DATABASE OF BIOTRANSFORMATIONS

Metabolite

Metabolite is a complete metabolism information system containing key 
information about metabolic transformations of xenobiotic compounds 
>from the literature and a registration system to input proprietary
metabolism studies.  Information in the database was abstracted from 
Biotransformation of Drugs (1977-1983), Pharmacokinetics (1986-
1990), and original metabolism literature from 1990 onwards.  
Metabolite is released semiannually.  The database provides indexing of 
path and scheme information for the metabolic transformations and 
includes data on species, route of administration and excretion, 
analytical methodology, parent compound class and physiological 
activity.


REACTION DATABASES

The ChemInform Reaction Library (ChemInform RXL)

ChemInform RXL is a collection of 371,000 novel syntheses and 
preparative methods in organic chemistry from 1946 onwards.  The 
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ChemInform RXL is updated with approximately 50,000 reactions 
annually and covers the following areas of chemistry: 
1.  new reactions, including enzymatic or microbial processes
2.  applications of known methods to the synthesis of new compounds
3.  improved synthetic methods and application of new reagents
4.  syntheses of natural products of general importance
5.  use of novel organo-element compounds and catalysts in synthesis

The Reference Library of Synthetic Methodology

The Reference Library is a collection of 170,000 innovative and 
significant reactions in the synthetic literature from 1946 to 1990.  The 
focus is on novelty of methodology and the best reaction has been 
selected to represent a specific methodology.

Current Synthetic Methodology (CSM)

Current Synthetic Methodology is a selection of significant reactions to 
synthetic chemists.  It consists of approximately 7,000 new reactions 
each year from ChemInform RXL from 1992 onwards. The focus of 
the database is: 
1.  new reagents or important modifications of known reagents
2.  chemo-, regio-, and stereo-selective reactions
3.  new synthetic methodology, emphasizing reactions of general use

REACCS-JSM 

REACCS-JSM contains new methods for organic synthesis abstracted 
>from the primary chemical and patent literature from 1980 onwards.
The database is an electronic version of Derwent s Journal of Synthetic 
Methods.  The focus of the database is novel functional group and ring 
chemistry, protecting group chemistry, and heterocyclic chemistry.  The 
database is updated with approximately 3,000 new reactions each year.

Comprehensive Heterocyclic Chemistry (CHC) 

CHC is a compendium of heterocyclic chemistry published in the 
chemical literature through 1983.  The source of the information in the 
database is Comprehensive Heterocyclic Chemistry, 1984. The 
database focuses on synthesis of heterocycles, reactions of heterocyclic 
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ORGSYN 

ORGSYN contains proven high-yield synthetic methods and 
preparations of specific compounds of broad interest to synthetic 
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For more information on these databases, please call 1-800-635-0064.

Best regards,

Dale Mehl
Director of Marketing
Database Business Unit
MDL Information Systems

dm@mdli.com





From virtual@quantum.larc.nasa.gov  Thu Dec  1 10:16:24 1994
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	by www.ccl.net (8.6.9/930601.1506) id JAA16096; Thu, 1 Dec 1994 09:41:44 -0500
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Message-Id: <199412011442.AA289842974@quantum.larc.nasa.gov>
Date: Thu, 1 Dec 1994 09:42:54 -0500
From: "Don H. Phillips" <virtual@quantum.larc.nasa.gov>
To: chemistry@ccl.net
Subject: Pentium Bug


In considering and discussing the possibilities of serious errors
arising from the Pentium division bug, it is important to be clear
about absolute and relative errors, the nature of the bug itself,
and the nature of the calculation.

About the bug:

1.  It bites infrequently, once every several billion divides if the
    numbers involved in the calculation are chosen by a truly random
    process.

2.  The error (bite) is usually (relatively) small but can be (relatively)
    large.  The largest relative error reported thus far was (6.1*10^-05).

About ab initio calculations:

1.  Very large quantities of numbers are calculated and processed.  The
    numbers processed vary very widely in absolute size.

2.  Different types of calculations (CI, MP, analytical or numerical energy
    derivative, SCF, etc) involve different types of intensive calculations.
    Some calculations approach numerical instability with the precision
    used for integrals, etc ( approaching *numerical* linear dependence
    with large basis sets, for example).

Some of the discussion on this list has focused on the large number of
quantities (two electron integrals) which have small absolute size.  It
is true that relative errors, even as large so as to leave only 4 significant
digits, are not important if the absolute value of the quantity under
consideration is near the numerical threshold of the calculation.

However, even after we discount the operations involving numbers within
a factor of 10^4 of the threshold we are left with a large number of
operations which might hit the bug and *might* lead to a significant error.

The analogy of the computations to weighing a captain by weighing the
ship and captain and subtracting the weight of the ship is a little
oversimplified for this discussion unless you consider that one of the
two weights may be in error by a factor which may be as large as
( 1 - 1*10^-4).  (How many *TONS* did you say the captain weighs?)

To spruce up the analogy you might consider a ship composed of nearly
equal amounts of positive and negative mass with the NET mass of
a supertanker.  Instead of weighing the ship, you must imagine cutting
up the ship two different ways and weighing the parts, including the
filings resulting from the cutting, independently. Include the captain
in one of the weighings.  The (signed) weights are summed twice, once
using the weights including the captain and once using the weights
without the captain.  If some fraction of the weights of the filings
are off by 10^-4 or less, the two sums will still have sufficient
accuracy for the difference to be a good approximation to the captain's
weight, but if the value for just one of the large pieces is significantly
in error, all bets are off.

A few years back, I saw reports that indicated that about 20% of the
cycles at the NSF supercomputer sites were being used for calculations
on molecules and solids.  Today, we most certainly have a much larger
volume of calculations being carried out on small (but powerful)
computers.  Some of the calculations take days, weeks, and even months
of cpu time.  It is inevitable that if enough calculations are being
carried out on Pentium cpus, some of them will contain significant errors.
The fact that one or more particular sets of calculations of particular
types were carried out without detecting an error, or only detecting
inconsequential errors, has limited relevance to the issue.  In
order to consider this error inconsequential, we would have to know
that the probability of an error of a given size be on the order of
that for an error of the same size occurring due to multiple bit memory
errors.  I don't believe that the available evidence supports such a
conclusion at this time.

I know of three cases in which powerful computers, operating in production
environments, had broken hardware producing bad values for weeks or months.
These cases involved a hot bit in a disk buffer on a Cray, a broken
vector multiplier on a Cray, and a broken vector adder on a Convex.  In
each case only a couple of users realized anything was wrong. Getting
the machine out of production for repair required that a user *prove*
that the machine had a problem.  In each case, dozens or hundreds of
persons were getting questionable results from the machines
without realizing it.  If Intel continues to require that users prove
that their applications have a problem with the Pentium divide error
in order to obtain a "repair", there are going to be a lot of machines
producing questionable results for a long time.

Don

From gerson@VNET.IBM.COM  Thu Dec  1 12:25:56 1994
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   with BSMTP id 3223; Thu, 01 Dec 94 12:05:50 EST
Date: Thu, 01 Dec 94 12:05:50 EST
To: chemistry@ccl.net
Subject: IBM Offers Added Customer Protection for Systems


From: Dennis J. Gerson, Ph.D.
      Technical Market Support; Chemical Sciences
      ---------------------------------------------------
Subject: IBM Offers Added Customer Protection for Systems

The following press release was issued by IBM today regarding the
Pentium problem and systems replacements.  I am posting this on the
CHEMISTRY MAILSERV because of the interest in this issue and in
response to numerous email messages from my colleagues on "what is
IBM planning to do about this".

Regards, Dennis Gerson

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

IBM Offers Added Customer Protection for Systems
with Pentium Microprocessors

November 30, 1994

IBM today announced that it will implement a series of programs
designed to assist customers who experience a problem with Intel
Pentium* microprocessors in IBM systems.

Intel last week acknowledged a defect in its Pentium
microprocessor that can cause inaccurate results in some
mathematical applications.  Like Intel, IBM expects a very
small number of customers to be affected. IBM is taking
extra steps to ensure that all its customers are protected.

In addition to working closely with Intel to resolve
the issue, IBM will for its customers and business partners:

     - Establish telephone numbers worldwide to help
       customers determine if they have a problem, and work
       with them to implement an appropriate resolution.

     - Upon customer need, provide for replacement of
       Pentium chips.

     - Add an informational letter to all products shipped
       with a Pentium processor.

Effective December 1 at 9:00 a.m., customers in the U.S. can
call 800-426-3389 for more information.

* Trademark of the Intel Corporation.

---------------------------------------------------------------
IBM POWER Parallel Systems Division |Tele:(214)406-7267 Fax:7246
1503 LBJ Freeway MS/280750          |IBMLINK: USIB5MSK @ IBMMAIL
Dallas TX 75234  USA                |Email: gerson@vnet.ibm.com

From jle@toyota.wavefun.com  Thu Dec  1 14:16:23 1994
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From: "Joe Leonard" <jle@toyota.wavefun.com>
Message-Id: <9412011050.ZM5217@toyota.wavefun.com>
Date: Thu, 1 Dec 1994 10:50:44 -0800
Reply-To: jle@wavefun.com
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
To: chemistry@ccl.net
Subject: Vendor-related support questions
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0


Folks,

	In spite of some initial problems with our Internet provider (which
were resolved basically by switching providers), Wavefunction Inc. is on the
net.  Questions can be directed to

	sales@wavefun.com
or
	support@wavefun.com

as appropriate.   Please let me/us know if there is any further problems when
emailing Wavefunction.

-- 

------------------------------------------------------------------------
Joe Leonard
Wavefunction Inc.
18401 Von Karman, Suite 370
Irvine, CA  92715                       I am a professional...
714-955-2120                                    do not attempt this at home.
714-955-2118 fax
jle@wavefun.com



From psubram@texaco.com  Thu Dec  1 15:16:31 1994
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Date: Thu, 1 Dec 94 14:12:41 CST
From: psubram@texaco.com (Palavo Subramanian)
Message-Id: <9412012012.AA27050@texaco.com>
To: chemistry@ccl.net
Subject: Polymer Chain Rigidity



 What is a good way to 'quantify' polymer chain rigidity ?. I am looking
at comparing the rigidity of Polymer A as a function of temperature and
also as a function of composition(monomer ratio in the case of a copolymer).
Is there a good way to calculate this? Is Persistence Length a good measure
of the rigidity?

 You can either post your replies on the net or mail to me at
psubram@texaco.com.  I will post a summary of the replies that I get.

Thanks in advance,

--Mani--

From janr@tiger.chem.uw.edu.pl  Thu Dec  1 16:17:13 1994
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Date: Thu, 1 Dec 1994 21:54:47 +0100
From: janr@tiger.chem.uw.edu.pl (Jan Radomski)
Message-Id: <9412012054.AA10952@tiger.chem.uw.edu.pl>
To: chemistry@ccl.net
Subject: Center-line C++ debugger
Cc: janr@tiger.chem.uw.edu.pl



-----
Dear Netters,
can some kind soul mail me direct about most recent
version of the Centerline Software C++ full screen
debugger? The last time I saw it working was about
year ago.

Jan Radomski

From walterse@mis.fuhscms.edu  Thu Dec  1 16:26:32 1994
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Message-Id: <199412012019.PAA24223@www.ccl.net>
Subject: hydride transfer to NAD...
To: CHEMISTRY@ccl.net
Date: Thu, 1 Dec 1994 14:24:29 -0600 (CST)
From: "Dr. D.Eric Walters" <walterse@mis.fuhscms.edu>
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Netters:

Is anyone aware of information on transition state geometry for hydride 
transfer to the nicotinamide ring of NAD?  I will appreciate any 
theoretical and/or experimental info you can provide.  Thanks!

Eric  Walters

* D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry
* Finch University of Health Sciences/The Chicago Medical School
* 3333 Green Bay Road, North Chicago, IL  60064
* ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.fuhscms.edu
* "A man would do nothing if he waited until he could do it so well that
*  no one would find fault with what he had done." --Cardinal Newman



From hinsenk@ERE.UMontreal.CA  Thu Dec  1 18:16:28 1994
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Date: Thu, 1 Dec 94 17:21:50 -0500
From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad)
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To: JeanLuc.Verschelde@rug.ac.be
Cc: CHEMISTRY@ccl.net
In-Reply-To: <Pine.SOL.3.91.941201113156.25462A-100000@allserv> (message from Jean-Luc Verschelde on Thu, 1 Dec 1994 11:36:38 +0100 (MET))
Subject: CCL: Brownian Dynamics


Jean-Luc Verschelde wrote:

	   I want to simulate the large scale movements of the lid
	   on horse pancreatic lipase . Therefore I need a brownian
	   dynamics algorithm .
	   Where can I find this algorithm and do you agree that this
	   algorithm is the best for this problem?

The classical reference for Brownian Dynamics is

  D.L. Ermak and J.A. McCammon
  Brownian Dynamics with hydrodynamic interactions
  J. Chem. Phys. 69, 1352 (1978)

Since I don't know anything about the system you want to study,
I can't give a "yes" or "no" about the suitability of this
method for you. However, I can give some general considerations:

- One condition is that the molecule you are studying is much
  larger than the molecules of the solvent around it. This is
  necessary to treat the solvent as a continuous liquid. It turns
  out that empirically this assumption is valid for much smaller
  molecules than one would expect, so this is probably not a
  problem for you.

- The second condition is that the velocity of your molecule
  relaxes on a faster timescale than the one on which it
  moves. The relaxation time is the quotient of the mass
  of your molecule and its friction coefficient in the
  solvent. If you know these values and the typical timescale
  of observable motion, you can easily verify this condition.
  If it is not fulfilled, but the first one is, you can still
  use Langevin dynamics.

- The Brownian Dynamics algorithm derived by Ermak & McCammon
  covers only translational motion. If you want to study
  molecules that do not have (approximately) spherical
  symmetry, you must also consider rotational motion. It is
  certainly possible to derive a similar equation of motion
  for rotation, but as far as I know this has not been done.

- If the Peclet number for your system, defined as UL/D, where
  U is the typical velocity (on the long time scale), L is
  the size of your molecule (or whatever part of it that
  moves), and D is the corresponding diffusion coefficient,
  is much larger than 1, then the random displacements and
  the derivative of the diffusion matrix can be neglected
  compared to the influence of other forces. In this case,
  called Stokesian Dynamics, both translational and
  rotational equations of motion are available. It is also
  much cheaper.

- The paper by Ermak & McCammon uses a very simple approximation
  to describe hydrodynamic interactions. In addition to being
  inaccurate, it has also a more fundamental problem (the
  diffusion matrix is not always positive definite). Better
  calculation schemes are available, but much more expensive
  in terms of CPU time.

-------------------------------------------------------------------------------
Konrad Hinsen                     | E-Mail: hinsenk@ere.umontreal.ca
Departement de Chimie             | Tel.: +1-514-343-6111 ext. 3953
Universite de Montreal            | Fax:  +1-514-343-7586
C.P. 6128, succ. A                | Deutsch/Esperanto/English/Nederlands/
Montreal (QC) H3C 3J7             | Francais (phase experimentale)
-------------------------------------------------------------------------------



From CHMIGORN@NUSVM.NUS.SG  Thu Dec  1 22:16:30 1994
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From: "I.Novak" <CHMIGORN%NUSVM.BITNET@phem3.acs.ohio-state.edu>
Subject: HP 712 VS. IBM POWERPC ON GAUSSIAN 92
To: CHEMISTRY@ccl.net
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Dear Netters,
I am trying to get some info about the ease of installation and
performance of Gaussian 92 on HP 712/60 and IBM PowerPC 40P
platforms. I will summarize the responses since perhaps some
people with tight funding may consider purchasing these two
low-end machines. Thanks!
Dr I.Novak,Dept.of Chemistry,NAtional University of Singapore
Sinagapore 0511
Internet:chmigorn@nus.sg
Bitnet: chmigorn@nusvm
P.S. Any reports of bugs and hitches would be especially welcome.

