From chemistry-request@server.ccl.net Fri Dec 14 08:07:56 2001
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Date: Fri, 14 Dec 2001 15:07:27 +0200 (EET)
From: Arvydas Tamulis <tamulis@itpa.lt>
To: <chemistry@ccl.net>
Subject: DALTON calculations.
Message-ID: <Pine.BSF.4.31.0112141458480.14870-100000@mserv.itpa.lt>
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Dear Madames, Sirs,

I would like to perform EPR calculations applied DALTON programme package
using Ames Laboratory basis set.
I prepared the below mentioned input files, but my traying was not
successful due to "errors in the input file". May be you explain me how
prepared required files to perform EPR calculations.
Thank you in advance,
J. Tamuliene

////////////////////////////////////////////////
INTGRL
ErSc2N
doublet geometry
    4               * 1.00D-15
        7.    1    2    2    1
N     0.         0.        0.
  20    2
     3260308.300        0.3831432510E-06    0.8442292180E-07
     666094.2500        0.2133549210E-05    0.4702641880E-06
     157037.1600        0.1214353360E-04    0.2675617870E-05
     42265.05500        0.5657385170E-04    0.1247139370E-04
     12820.26000        0.2288999530E-03    0.5044672760E-04
     4319.775400        0.8129533860E-03    0.1793884020E-03
     1592.062900        0.2596581360E-02    0.5735646950E-03
     631.8305400        0.7570379080E-02    0.1680537650E-02
 ............
\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
**DALTON INPUT
.RUN PROPERTIES
**WAVE FUNCTIONS
.HF
**PROPERTIES
.MOLGFA
*END OF INPUT


From chemistry-request@server.ccl.net Fri Dec 14 04:26:10 2001
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From: Dearden John <J.C.Dearden@livjm.ac.uk>
To: "'qsar_society@accelrys.com'" <qsar_society@accelrys.com>,
   David Konerding <dek@cgl.ucsf.edu>, chemistry@ccl.net
Subject: RE: QSAR - Re: CCL:somewhat obscure chemistry quote
Date: Fri, 14 Dec 2001 09:25:42 -0000
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A few more quotable quotes:

"We are perhaps not far removed from the time when we shall be able to
submit the bulk of chemical phenomena to calculation": J.L. Gay-Lussac,
1808.

"All of chemistry, and with it crystallography, would become a branch of
mathematical analysis which, like astronomy, taking its constants from
observation, would enable us to predict the character of any new compound
and possibly the source from which its formation may be anticipated":
Charles Babbage, 1838.

"It is the mark of an instructed mind to rest easy with the degree of
precision which the nature of the subject permits, and not to seek an
exactness where only an approximation of the truth is possible": Aristotle,
384-322 BC.

"Amid all the uncertainties, even a clouded crystal ball is of value":
Anonymous.

My favourite of all, which came from Al Leo, is part of a poem by an
American poet, Edna St. Vincent Millay:

"Upon this gifted age rains from the sky
A meteoric shower of facts.....
They lie unquestioned, uncombined.
Wisdom enough to leech us of our ills
Is daily spun, but there exists
No loom to weave it into fabric".

Happy Christmas, everybody.

John Dearden

>-----Original Message-----
>From: Osman F. Guner [mailto:osman@accelrys.com]
>Sent: 12 December 2001 18:30
>To: David Konerding; chemistry@ccl.net
>Cc: qsar_society@accelrys.com
>Subject: QSAR - Re: CCL:somewhat obscure chemistry quote
>
>
>NB: Unless you reset the To: line, your reply goes to the entire list
>---
>
>
>"Every attempt to employ mathematical methods in the study of chemical 
>questions must be considered profoundly irrational and contrary to the 
>spirit of chemistry.  If mathematical analysis should ever 
>hold a prominent 
>place in chemistry --an aberration which is happily almost 
>impossible-- it 
>would occasion a rapid and widespread degeneration of that science."
>A. Compte, 1798-1857
>
>There are some positive quotes from the same time period as well:
>
>"The more progress physical sciences make, the more they tend 
>to enter the 
>domain of mathematics, which is a kind of centre to which they all 
>converge.  We may even judge the degree of perfection to which 
>a science 
>has arrived by the facility with which it may be submitted to 
>calculation."
>A. Quetelet, 1796-1874
>
>Unfortunately, I have misplaced the actual references.  Hope 
>this helps...Osman
>
>At 09:57 AM 12/12/2001, David Konerding wrote:
>
>>I'm looking for the source of a somewhat obscure chemistry 
>quote I once
>>came across but cannot find definitevly.  I think it was 
>written by a 19th
>>century chemist who thought that math/computation in 
>chemistry was wholly
>>inappropriate.  Does this ring a bell for anybody?
>>
>>Thanks.
>>--------------------------------------------------------------
>---------------
>>David Konerding
>>Email: dek@cgl.ucsf.edu
>>WWW: http://www.cgl.ucsf.edu/home/dek
>>--------------------------------------------------------------
>---------------
>>
>>
>>-= This is automatically added to each message by mailing script =-
>>CHEMISTRY@ccl.net -- To Everybody  | 
>CHEMISTRY-REQUEST@ccl.net -- To Admins
>>MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
>>CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: 
>gopher.ccl.net 70
>>Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | 
>Jan: jkl@ccl.net
>
>---
>Osman F. Güner, Ph.D.
>Director,  Lead Identification & Optimization
>Accelrys Inc.   (858) 799-5341
>osman@accelrys.com        http://www.accelrys.com
>
>_______________________________________________
>qsar_society mailing list
>qsar_society@accelrys.com
>http://nntp-mailman.sd.accelrys.com/mailman/listinfo/qsar_society
>


From chemistry-request@server.ccl.net Fri Dec 14 04:02:13 2001
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From: =?iso-8859-1?q?thenmalar=20rathinavelan?= <thenmalrr@yahoo.co.in>
Subject: difference between Gibbs and MM_PBSA
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Dear gentlepersons,
   I have planned to carry out free energy
calculations using Amber6.0. In relation to this I
like to know what is the difference in calculating the
free energy using Gibbs module and MM-PBSA and which
is more reliable one. Since I am a new user to this I
like to learn the basic regarding these two and please
suggest me proper reference for this.
 
Thank you very much

With Best regards,
Thenmalar


________________________________________________________________________
For Stock Quotes, Finance News, Insurance, Tax Planners, Mutual Funds...
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From chemistry-request@server.ccl.net Fri Dec 14 01:30:46 2001
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From: chem@oxygen.chem.nthu.edu.tw
To: "Dr. Daniel Glossman-Mitnik" <daniel.glossman@cimav.edu.mx>
Cc: Computational Chemistry List <CHEMISTRY@ccl.net>
Subject: Re: CCL:G98 compilation problems on LINUX
Message-ID: <20011214143027.A19623@OXYGEN.chem.nthu.edu.tw>
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In-Reply-To: <007a01c1842b$5beb6c20$2601010a@cimav.edu.mx>; from daniel.glossman@cimav.edu.mx on Thu, Dec 13, 2001 at 03:10:30PM -0800

On Thu, Dec 13, 2001 at 03:10:30PM -0800, Dr. Daniel Glossman-Mitnik wrote:
> Dear netters:
> 
> I am trying to compile the g98 source code (rev A9) on a Pentium 3
> 800 running  Redhat 7.2. I have installed the Portland Group f77
> compiler and I have put the blas-f2c.a and blas-opt.a files in
> /usr/local/lib.
> The compilation seems to run fine up to a point where it bombs. As I
> have no previous experience I don´t know what the messages mean
> and thus what action to follow.
> 
> I including the last lines of the bldg98.log file.  Any help would be
> appreciated.
> 

Apprantly you failed to compile bsd/mdutil.c at earlier stage.
try to find the string "mdutil.c" in your bldg98.log file and see what
had happened previously.


--
Yu, Jen-Shiang Kenny  	//	jsyu@Platinum.chem.nthu.edu.tw
http://oxygen.chem.nthu.edu.tw/~jsyu
Theoretical Chemistry Lab,
Department of Chemistry,
National Tsing Hua University
Hsinchu 300, TAIWAN




From chemistry-request@server.ccl.net Fri Dec 14 05:59:20 2001
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To: chemistry@ccl.net
Date: Fri, 14 Dec 2001 11:58:40 +0100
Subject: CCL: - somewhat obscure chemistry quote
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Osman F. Guner:

> My all time favorite quote is actually from Niels Bohr, I think:
> 
> "Prediction is very difficult... especially about the future."

This is a quotation from the Danish humorist and cartoonist Robert
Storm Petersen, known as "Storm P". Niels Bohr was probably fond of 
it!

http://www.rene.belso.dk/StormP1.html

Yours, Jens >--<

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
JENS SPANGET-LARSEN         Office:     +45 4674 2710
Department of Chemistry     Fax:        +45 4674 3011
Roskilde University (RUC)   Cell-Phone: +45 2320 6246
P.O.Box 260                 E-Mail: JSL@virgil.ruc.dk
DK-4000 Roskilde, Denmark   http://virgil.ruc.dk/~jsl
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-


From chemistry-request@server.ccl.net Fri Dec 14 09:45:24 2001
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Date: Fri, 14 Dec 2001 09:45:11 -0500 (EST)
From: Jan Labanowski <jkl@ccl.net>
To: Jorge Gancheff <jorge@bilbo.edu.uy>
cc: Jan Labanowski <jkl@ccl.net>, chemistry@ccl.net
Subject: Re: Lebedev Integration grid
In-Reply-To: <Pine.A32.3.96.1011214113815.6022A-100000@bilbo.edu.uy>
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To to www.ccl.net, click on Text Search link and type in:
lebedev

Or just use this link:
http://server.ccl.net/cgi-bin/ccl.search?config=htdig&restrict=&exclude=&method=and&format=long&words=lebedev

Jan K. Labanowski            |    phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center    |    Internet: jkl@ccl.net 
1224 Kinnear Rd,             |    http://www.ccl.net/chemistry.html
Columbus, OH 43212-1163      |    http://www.ccl.net/


On Fri, 14 Dec 2001, Jorge Gancheff wrote:

> Dear CCLers:
> 
> I would like to know if it is possible to obtain information of Labedev
> integration grid o something related.
> Regards,
> Jorge
> 
>  
>    ***********************************************************************  
> 			MSc. Jorge S.Gancheff
> 	        
>     Cátedra de Química Inorgánica	 e-mail: jorge@bilbo.edu.uy
>     Departamento "Estrella Campos"       Tel.: +598 2 924 9739	
>     Facultad de Química, UDELAR          Fax:  +598 2 924 1906
>     Montevideo, 11800			 URUGUAY	
>    *********************************************************************** 
> 




From chemistry-request@server.ccl.net Fri Dec 14 09:40:59 2001
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Date: Fri, 14 Dec 2001 11:40:37 -0300 (GRNLNDST)
From: Jorge Gancheff <jorge@bilbo.edu.uy>
To: chemistry@ccl.net
Subject: Lebedev Integration grid
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Dear CCLers:

I would like to know if it is possible to obtain information of Labedev
integration grid o something related.
Regards,
Jorge

 
   ***********************************************************************  
			MSc. Jorge S.Gancheff
	        
    Cátedra de Química Inorgánica	 e-mail: jorge@bilbo.edu.uy
    Departamento "Estrella Campos"       Tel.: +598 2 924 9739	
    Facultad de Química, UDELAR          Fax:  +598 2 924 1906
    Montevideo, 11800			 URUGUAY	
   *********************************************************************** 



From chemistry-request@server.ccl.net Fri Dec 14 09:33:02 2001
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From: Reinaldo Pis Diez <pis_diez@quimica.unlp.edu.ar>
Subject: Parallel programming: mpich vs pvm? -> Summary
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--=====================_358886866==_.ALT
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         Hi netters,

                 Some days ago I posted a mail seeking for a comparison 
between mpi and pvm wrt performance and ease to use/learn.
                 I got several answers and wish to thank Richard Gillilan, 
Chris Klein, Sigismondo Boschi, Marcel Swart, Huub van Dam, Konrad Hinsen, 
Mark Russell, and David Reichert.
                 First, I must say that mpich and pvm are not the only free 
tools to develop parallel code. LAM-MPI is another free implementation of 
MPI. OpenMP, Global Array Toolkit, and the Bulk Synchronous Parallel (BSP) 
model seem to be good alternatives although I don't know if these are free.
                 Second, it seems to be general agreement to put mpi-based 
tools over pvm. Both mpich and lam-mpi are highly recommended to start with.
                 Below are the corresponding answers.
                 Thanks a lot agains!!
                 Regards,

                                                                 Reinaldo

************* by Richard Gillilan *******************************

I would be interested to know what others think. I have not
coded in PVM, but have studied MPI (MPICH is one implementation
of MPI). MPI seems to be the most widely used now. I have been told
by persons using PVM that it is a good choice when your computing cluser
is heterogeneous.
By the way, the Cornell Theory Center is holding its annual
parallel computing virtual workshop. I took it last year. Though
they run a Win2K cluster, the material is generic and applicable
to any other system: www.tc.cornell.edu/services/edu/events/parallel/

********************by Chris Klein ************************************

another implementation of MPI is LAM-MPI. I am using that for parallel
amber on a linux cluster. Runs better than MPICH (for amber), but I do
not have any experiences with other parallel programs.
My impression is that PVM is considered a bit old-fashioned

********************by Sigismondo Boschi ************************************

PVM is the anchestor of MPI, in the sense J. Dongarra is the main author of 
both.
But PVM is a library, MPI is a standard - with its definition 
(www.mpi-forum.org) and the vendors can optimise it - the important is they 
do not violate the definitions. The best is to learn is MPI, maily because 
PVM is outmoded. However, MPI allow you to have higher performance with 
collective calls and non-blocking routines, and also higher "coding" 
perfomance since it has many high level features.

********************by Marcel Swart ************************************

In fact, you are wrong, there is even a third: LAM-MPI, and it is preferred 
over the other two.
First of all, because MPI is faster and much easier to learn and use than PVM;
second, because LAM-MPI is more stable (and faster) than MPICH.
It can be found at:
http://www.mpi.nd.edu/lam/

********************by Huub van Dam ************************************

MPICH is a freely available implementation of the MPI standard, the currently
dominant Message Passing Interface. PVM was the message passing library that
preceded it and I thought was pretty much dead by now (for good reasons). 
So from the choice of these 2 I would go for MPI.
However the message passing paradigm is not always the most natural 
approach to solving a parallel programming problem. Sometimes using a 
shared memory approach is better. OpenMP seems to popular in this arena 
although it has been applied with mixed success.
If you don't want to decide right now whether a shared memory approach or 
message passing approach is the best you can combine the ease of use of the 
shared memory programming with the high performance of message passing 
using the Global Array Toolkit (http://www.emsl.pnl.gov:2080/docs/global/) 
as developed at Pacific Northwest National Laboratory. However, you should 
have a good look around for a tutorial.

********************by Konrad Hinsen ************************************

Another free MPI implementation is LAM. MPICH and LAM both implement
MPI interface, either one will for for learning, and in most
circumstances there shouldn't be significant performance differences.
As for the choice between PVM and either MPI, I'd go for MPI. Both PVM
and MPI follow the same basic approach (message passing), and MPI is
an industry standard, whereas PVM is not.
However, there is a real alternative worth looking at, the BSP model,
for which there are two implementations, BSPlib from Oxford and PUB
> from Paderborn. BSP (which stands for Bulk Synchronous Parallel) is a
higher-level abstraction than the message-passing model which is the
basis of MPI and PVM. It is much simpler to use and especially to
debug (deadlocks are impossible, for example), and its long-time users
also claim that it permits better communications optimization within
the BSP library. See www.bsp-worldwide.org for more information about
BSP.

********************by Mark Russell ************************************

There is also a library based on the MPI system called 'Lam' - at Notre
Dame University I think? Its standard with most recent Linux
distributions.
The question of which to use, depends on what models you want. PVM is the
older model and I think was designed more for homogenous networks. MPI
(both MPICH and LAM) is the newer standard and is the best for
heterogenous networks.
My opinion is that the MPI is the one to go for, seems to be the one with
the biggest future (until the next one comes along!). The question
between MPICH and LAM is difficult, as everyone has their own favourite.
Personally, I prefer LAM, but I'm sure that you will get mails from other
people who say otherwise! ;-) Fitting MPI into a program is pretty
simple when your learning parallel, though I would recommend getting some
'serious' books on it before jumping in the deep-end. There are lots of
pit-falls and 'tricks' in the system that can be daunting to start with.

********************by David Reichert ************************************

Well that's an interesting question, my gut feeling is that MPI/MPICH is
used more often than PVM. There's a paper comparing the two on the PVM web
site "PVM and MPI: a comparison of Features" by G.A. Geist, J,A. Kohl, and
P.M. Papadopoulos that you may find helpful.
hope that helps,

--=====================_358886866==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Hi
netters,<br><br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Some
days ago I posted a mail seeking for a comparison between mpi and pvm wrt
performance and ease to use/learn. <br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>I
got several answers and wish to thank Richard Gillilan, Chris Klein,
Sigismondo Boschi, Marcel Swart, Huub van Dam, Konrad Hinsen, Mark
Russell, and David Reichert. <br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>First,
I must say that mpich and pvm are not the only free tools to develop
parallel code. LAM-MPI is another free implementation of MPI. OpenMP,
Global Array Toolkit, and the Bulk Synchronous Parallel (BSP) model seem
to be good alternatives although I don't know if these are free. <br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Second,
it seems to be general agreement to put mpi-based tools over pvm. Both
mpich and lam-mpi are highly recommended to start with.<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Below
are the corresponding answers.<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Thanks
a lot agains!!<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Regards,&nbsp;
<br><br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Reinaldo<br><br>
************* by Richard Gillilan
*******************************<br><br>
I would be interested to know what others think. I have not <br>
coded in PVM, but have studied MPI (MPICH is one implementation <br>
of MPI). MPI seems to be the most widely used now. I have been told 
<br>
by persons using PVM that it is a good choice when your computing cluser
<br>
is heterogeneous. <br>
By the way, the Cornell Theory Center is holding its annual <br>
parallel computing virtual workshop. I took it last year. Though <br>
they run a Win2K cluster, the material is generic and applicable <br>
to any other system:
<a href="http://www.tc.cornell.edu/services/edu/events/parallel/" eudora="autourl"><font color="#0000FF"><u>www.tc.cornell.edu/services/edu/events/parallel/<br><br>
</a></u></font>********************by Chris Klein
************************************<br><br>
another implementation of MPI is LAM-MPI. I am using that for parallel
<br>
amber on a linux cluster. Runs better than MPICH (for amber), but I do
<br>
not have any experiences with other parallel programs. <br>
My impression is that PVM is considered a bit old-fashioned<br><br>
********************by Sigismondo Boschi
************************************<br><br>
PVM is the anchestor of MPI, in the sense J. Dongarra is the main author
of both. <br>
But PVM is a library, MPI is a standard - with its definition
(<a href="http://www.mpi-forum.org/" eudora="autourl"><font color="#0000FF"><u>www.mpi-forum.org</a></u></font>)
and the vendors can optimise it - the important is they do not violate
the definitions. The best is to learn is MPI, maily because PVM is
outmoded. However, MPI allow you to have higher performance with
collective calls and non-blocking routines, and also higher
&quot;coding&quot; perfomance since it has many high level
features.<br><br>
********************by Marcel Swart ************************************
<br><br>
In fact, you are wrong, there is even a third: LAM-MPI, and it is
preferred over the other two. <br>
First of all, because MPI is faster and much easier to learn and use than
PVM; <br>
second, because LAM-MPI is more stable (and faster) than MPICH.<br>
It can be found at: <br>
<font color="#0000FF"><u><a href="http://www.mpi.nd.edu/lam/" eudora="autourl">http://www.mpi.nd.edu/lam/<br><br>
</a></u></font>********************by Huub van Dam
************************************ <br><br>
MPICH is a freely available implementation of the MPI standard, the
currently <br>
dominant Message Passing Interface. PVM was the message passing library
that <br>
preceded it and I thought was pretty much dead by now (for good reasons).
So from the choice of these 2 I would go for MPI.<br>
However the message passing paradigm is not always the most natural
approach to solving a parallel programming problem. Sometimes using a
shared memory approach is better. OpenMP seems to popular in this arena
although it has been applied with mixed success.<br>
If you don't want to decide right now whether a shared memory approach or
message passing approach is the best you can combine the ease of use of
the shared memory programming with the high performance of message
passing using the Global Array Toolkit
(<a href="http://www.emsl.pnl.gov:2080/docs/global/" eudora="autourl"><font color="#0000FF"><u>http://www.emsl.pnl.gov:2080/docs/global/</a></u></font>)
as developed at Pacific Northwest National Laboratory. However, you
should have a good look around for a tutorial.<br><br>
********************by Konrad Hinsen ************************************
<br><br>
Another free MPI implementation is LAM. MPICH and LAM both implement
<br>
MPI interface, either one will for for learning, and in most <br>
circumstances there shouldn't be significant performance
differences.<br>
As for the choice between PVM and either MPI, I'd go for MPI. Both PVM
<br>
and MPI follow the same basic approach (message passing), and MPI is
<br>
an industry standard, whereas PVM is not.<br>
However, there is a real alternative worth looking at, the BSP model,
<br>
for which there are two implementations, BSPlib from Oxford and PUB 
<br>
> from Paderborn. BSP (which stands for Bulk Synchronous Parallel) is a
<br>
higher-level abstraction than the message-passing model which is the
<br>
basis of MPI and PVM. It is much simpler to use and especially to <br>
debug (deadlocks are impossible, for example), and its long-time users
<br>
also claim that it permits better communications optimization within
<br>
the BSP library. See
<a href="http://www.bsp-worldwide.org/" eudora="autourl"><font color="#0000FF"><u>www.bsp-worldwide.org</a></u></font>
for more information about <br>
BSP.<br><br>
********************by Mark Russell ************************************<br><br>
There is also a library based on the MPI system called 'Lam' - at Notre <br>
Dame University I think? Its standard with most recent Linux <br>
distributions.<br>
The question of which to use, depends on what models you want. PVM is the <br>
older model and I think was designed more for homogenous networks. MPI <br>
(both MPICH and LAM) is the newer standard and is the best for <br>
heterogenous networks. <br>
My opinion is that the MPI is the one to go for, seems to be the one with <br>
the biggest future (until the next one comes along!). The question <br>
between MPICH and LAM is difficult, as everyone has their own favourite. <br>
Personally, I prefer LAM, but I'm sure that you will get mails from other <br>
people who say otherwise! ;-) Fitting MPI into a program is pretty <br>
simple when your learning parallel, though I would recommend getting some <br>
'serious' books on it before jumping in the deep-end. There are lots of <br>
pit-falls and 'tricks' in the system that can be daunting to start with.<br><br>
********************by David Reichert ************************************<br><br>
Well that's an interesting question, my gut feeling is that MPI/MPICH is <br>
used more often than PVM. There's a paper comparing the two on the PVM web <br>
site &quot;PVM and MPI: a comparison of Features&quot; by G.A. Geist, J,A. Kohl, and <br>
P.M. Papadopoulos that you may find helpful. <br>
hope that helps,<br>
</html>

--=====================_358886866==_.ALT--



From chemistry-request@server.ccl.net Fri Dec 14 09:57:33 2001
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From: "Phil Hultin" <hultin@cc.UManitoba.CA>
To: "Computational Chemistry List" <chemistry@ccl.net>
Subject: Who said anything about GUI?
Date: Fri, 14 Dec 2001 08:57:11 -0600
Message-ID: <MFEKIFDLINLMPCOPEBDGGEACCCAA.hultin@cc.umanitoba.ca>
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OK CCL, repeat after me:

"User-friendly is not a synonym for GUI.  GUI is not a synonym for
User-friendly."

Konrad Hinsen said it a few postings ago:

>Finally, a good user interface isn't necessarily a graphical one, nor
>a simple one. A good user interface is one that lets users express
>their computations in terms of concepts that they are familiar with
>and without arbitrary complexities (such as inconsistent syntax).
>Meaningful error reporting is another important issue.

This is all I have to say on the issue.

Dr. Philip G. Hultin
Associate Department Head and
Associate Professor of Chemistry
University of Manitoba
Winnipeg, MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:hultin@cc.umanitoba.ca
http://www.umanitoba.ca/chemistry/


From chemistry-request@server.ccl.net Fri Dec 14 10:39:06 2001
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Subject: Re: CCL:Parallel programming: mpich vs pvm? -> Summary
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Reinaldo Pis Diez <pis_diez@quimica.unlp.edu.ar> writes:

>                  First, I must say that mpich and pvm are not the only
> free tools to develop parallel code. LAM-MPI is another free
> implementation of MPI. OpenMP, Global Array Toolkit, and the Bulk
> Synchronous Parallel (BSP) model seem to be good alternatives although
> I don't know if these are free.

The Global Array Toolkit is free, as are the two BSP implementations
that I mentioned. OpenMP is not a product, but a convention, it is
implemented by compilers. I am not aware of any free compilers that
implement OpenMP.

Also, OpenMP is for shared memory machines, the other libraries are
for distributed memory machines. You can always use distributed-memory
tools on shared-memory machines, but the other direction doesn't work.
A more general (but more difficult) alternative to OpenMP for shared
memory systems is manual coding of a multithreaded application.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------

From chemistry-request@server.ccl.net Fri Dec 14 11:07:53 2001
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Date: Fri, 14 Dec 2001 17:18:55 +0100
From: Cristina Ronzitti <ronzitti@crs4.it>
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Hi,
last month I sent a message to this list because I got nanq results from
my molecular dynamics simulation. I thought it was a wrong deltat...but
recently I realized there was an error in an input file: I attributed
(not for choice...) some dihedrals angles to water molecules...
I have corrected the error and now all is ok.
Thanks,
Cristina
-- 
____________________________________________________________________

Cristina Ronzitti
Degree: final-year in chemistry                                     
Chemical Processes and Material Modelling Area - Fuel Cells
Project           
CRS4 - VI strada ovest - Z.I. - Macchiareddu - UTA - Cagliari 
FAX:+39-070-2796216          
____________________________________________________________________

From chemistry-request@server.ccl.net Fri Dec 14 11:07:56 2001
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From: "Pablo Vitoria" <qibvigap@lg.ehu.es>
To: "CCL" <CHEMISTRY@ccl.net>
Subject: Strange things in AIMPAC
Date: Fri, 14 Dec 2001 17:05:43 +0100
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Hi all,

I have been using the AIMPAC programs for a while now, with (almost) no
problem. But in a couple of my last calculations I observed a strange
behaviour in PROAIMV: there is no error message, the job finishes, but the
output is broken like this (last lines of the output file):

Surface is done ...
Doing Integration Outside of Beta Sphere ...
2 x the default number of radial points used
Integration Outside of Beta Sphere is Done ...
RESULTS OF THE INTEGRATION
N 2.03901120165397E+01 NET CHARGE 2.60988798346031E+00
G 9.40097838081680E+02

There is nothing below the kinetic energy (G). Had anyone the same problem
before?

I must say that the I compiled PROAIMV increasing the number of atoms, basis
functions and primitives.

Thanks for any help
Best regards

Pablo

--------------------------------------------------------
Pablo Vitoria Garcia
Dpto. Química Inorgánica, Facultad de Ciencias
Universidad del País Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)

Tfno. 94 6015522
Fax. 94 4648500



From chemistry-request@server.ccl.net Fri Dec 14 11:12:46 2001
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Date: Fri, 14 Dec 2001 08:12:21 -0800
From: David Case <case@scripps.edu>
To: thenmalar rathinavelan <thenmalrr@yahoo.co.in>
Cc: CHEMISTRY@ccl.net
Subject: Re: CCL:difference between Gibbs and MM_PBSA
Message-ID: <20011214081221.C15811@gamow.scripps.edu>
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In-Reply-To: <20011214090148.632.qmail@web8006.mail.in.yahoo.com>; from thenmalrr@yahoo.co.in on Fri, Dec 14, 2001 at 09:01:48AM +0000

On Fri, Dec 14, 2001, thenmalar rathinavelan wrote:

>    I have planned to carry out free energy
> calculations using Amber6.0. In relation to this I
> like to know what is the difference in calculating the
> free energy using Gibbs module and MM-PBSA and which
> is more reliable one. Since I am a new user to this I
> like to learn the basic regarding these two and please
> suggest me proper reference for this.
>  

Free energy calculations, such as free energy perturbation or thermodynamic
integration, are potentially very accurate ways of estimating such
differences: with good sampling, they can be as good as the underlying force
fields themselves.

There are lots of good reviews and introductions.  My personal favorites
are:

   Frenkel and Smit, "Understanding Molecular Simulations" (Academic Press).

   Mezei and Beveridge, "Free Energy Simulations", Ann. NY Acad. Sci.
      482:1-23 (1986)

   Kollman, "Free energy calculations: applications to chemical and bio-
      chemical phenomena", Chem. Rev. 93:2395-2417 (1993).

(Of course, the last two are dated, and cover only the basics.)


The MM_PBSA approach takes snapshots from molecular dynamics simulations,
and re-evaluates the energies in a continuum solvent model; solute entropies
are estimated separately.  This model is more easily applicable to large
conformational changes (it does not require creating intermediate states),
but adds errors arrising from the continuum approximation and the entropy
model used those arising from the underlying force field.

My favorite overview of this method is the following:

   Kollman, et. al, Accts. Chem. Res. 33:889-897 (2000).

You should be aware that carefully setting up your system and working hard
to get adequate sampling are key to both methods.  In addition to the 
overviews mentioned above, you should carefully study reports of
applications that are close to the ones you plan to carry out, and should
plan to try to (approximately) reproduce some published results before
starting out on a new system.  Obtaining good estimates of free energy
differences from simulation is a very challenging task.

...hope this helps...please remember that this just represents my thinking,
and that there are in fact many good discussions of the subject available.

...regards...dac

-- 

==================================================================
David A. Case                     |  e-mail:      case@scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================


From chemistry-request@server.ccl.net Fri Dec 14 11:27:32 2001
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From: Jan Labanowski <jkl@ccl.net>
To: chemistry@ccl.net
cc: Jan Labanowski <jkl@ccl.net>, jgreer@nmrc.ucc.ie
Subject: 02.06.18 EMRS 2002 Symposium A:  Atomic Scale Materials Design
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Date: Fri, 14 Dec 2001 16:25:12 +0000
From: Jim Greer <jgreer@nmrc.ucc.ie>
To: mel@asdn.net
Subject: EMRS 2002 Symposium A

Symposium A - Atomic Scale Materials Design
European Materials Research Society
E-MRS Spring Meeting
June 18-21, 2002

Venue:
Congress Center
Palais de la Musique et des Congres
Strasbourg France

FINAL CALL FOR PAPERS
DEADLINE FOR ABSTRACT SUBMISSION: January 14, 2002

On-line submissions:
http://www-emrs.c-strasbourg.fr/abstract.html

Details of Symposia:
http://www-emrs.c-strasbourg.fr/2002_Spring_Ann2.pdf

Supported by the European Science Foundation and
the Psi_k Network

We seek submissions on electronic structure
calculations and computational material science
applied to:
· Microelectronics and Optoelectronic,
· Nanotechnology and Biotechnology
· Fine Chemicals and Drug Design
· Polymers
including
· Surfaces and interfaces
· Molecules and clusters
· Catalysis
· Biological molecules, macromolecules, polymers
· Plasmas, chemical vapor deposition, atomic layer deposition,
  and materials processing
· Nanostructures
We also seek submissions discussing advances in electronic structure
theory, which enable new problems to be investigated.



From chemistry-request@server.ccl.net Fri Dec 14 11:31:25 2001
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From: Ivan Rossi <ivan@biocomp.unibo.it>
To: CompChem Mailing List <chemistry@ccl.net>
Subject: 02.02.03 School: Protein Struct Predict, Bologna, IT: Programme
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We are pleased to announce you the Bologna Winter School 2002 final programme

PREDICTING THE 3D STRUCTURE OF DIFFICULT PROTEINS
Methods for the prediction of membrane protein structure and new fold
recognition of globular proteins

** Sponsored by European Science Foundation (ESF) **

Bologna, ITALY
3-9 February 2002,

School chairs:
Rita Casadio  and  Lanfranco Masotti

Scientific Committee
R. Casadio, D. Jones, B. Rost, A. Tramontano

Details: 
Main topics will be: prediction of membrane proteins, low homology protein
modelling, ab initio structure prediction, new fold recognition. Round table
discussions will focus on "hot" topics of protein structure prediction.

TEACHERS:

Pierre Baldi        (University of California, Irvine, USA)
Rita Casadio        (University  of  Bologna, Bologna, IT)
David T. Jones      (University College, London, UK)
Anders Krogh        (Technical University of Denmark, Lyngby, DK)
Arthur M. Lesk	    (University of Cambridge, Cambridge, UK)
Marc Marti'-Renom   (Rockefeller University, New York, USA)
Hartmut Michel      (Max Planck Institute of Biophysics, Frankfurt am Main, DE)
Burkhard Rost       (Columbia University, New York, USA)
Manfred Sippl	    (University of Salzburg, Salzburg, AT)
Michael Sternberg   (Imperial College, London, UK)
Mike Taussig	    (The Babraham Institute, Cambridge, UK)
Anna Tramontano     (University "La Sapienza", Roma, IT)
Alfonso Valencia    (National Centre of  Biotechnology, Cantoblanco, ES)
Michele Vendruscolo (Oxford Centre for Molecular Sciences, Oxford, UK)
Gunnar von Heijne   (University of Stockholm, Stockholm, SE)
Gert Vriend         (University of Nijmegen, Nijmegen, NL)
Stephen White       (University of California, Irvine, USA)

For Application send a short C.V. to  school@biocomp.unibo.it.
You will be notified by  e-mail of acceptance.

     Deadline for application is
     December 30, 2001

URL:
http://www.biocomp.unibo.it/school/html2002/
Contact information: school@biocomp.unibo.it.



School Programme

Monday 4
 8:30 - 9:00	Registration
 9:00 - 9:30	Opening remarks
 9:30 - 11:00	Hartmut Michel	
			Crystallization and structures of membrane
			proteins: routes and achievements
11:30 - 13:00	Arthur Lesk
			Protein folding: easy for nature, difficult for us
15:00 - 16:30	Stephen White
      			How membranes shape protein structure
17:00 - 18:30	Gert Vriend
               		What bioinformatics can say about G protein 
			coupled receptors

Tuesday 5
 9:30 - 11:00	Marc Martí-Renom
			How many protein structures can we predict with
			building by homology?                    
11:30 - 13:00 	Anna Tramontano
               		Pitfalls and advances in molecular modelling
15:00 - 16:30	Burkhard Rost
                        Predicting the structure of globular proteins                  
17:00 - 18:30	Alfonso Valencia
        		From the assignment of protein fold to the
			prediction of functional specificity

Wednesday 6
 9:30 - 11:00	Michael Sternberg
			Exploiting the protein structure in the
			post-genome era
11:30 - 13:00	David Jones
			Predicting protein folds for globular and
			membrane proteins
15:00 - 16:30	Manfred Sippl
			Structure based bioinformatics
17:00 - 18:30	Arthur Lesk
			Ab initio protein structure prediction: 
			the state of the art

Thursday 7 
 9:30 - 11:00	Pierre Baldi
			Machine learning methods for structural
			proteomics
11:30 - 13:00	Michele Vendruscolo
			Protein fold prediction using contact information
15:00 - 18:00	ROUND TABLE DISCUSSION

Friday 8 
 9:30 - 11:00	Gunnar von Heijne
			Membrane proteins: combining experiments
			and prediction for topology mapping
11:30 - 13:00 	Anders Krogh
			Hidden Markov Models and the prediction of
			the topology of membrane proteins                                          
15:00 - 16:30	Stephen White
			Energetics, stability and prediction of
			transmembrane helices
17:00- 18:30	Rita Casadio
			Predicting the structure of beta-barrel membrane
			proteins
18:30 - 19:00	Conclusive remarks

-- 
Dr. Ivan Rossi -  CIRB Biocomputing Unit
e-mail: ivan@biocomp.unibo.it   Web: http://www.biocomp.unibo.it/ivan




From chemistry-request@server.ccl.net Fri Dec 14 11:50:10 2001
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To: chemistry@ccl.net
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Subject: Dipoles
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A physical chemistry colleague uses Gaussian to compute structures and 
vibrational frequencies; he then animates the frequencies with Hyperchem, 
and also uses Hyperchem's ability to place little arrows describing the 
changes in the bond dipoles associated with a vibration.  He is interested 
to be able, essentially, to sum up all these little arrows to get the net 
dipole change for the molecule in a given mode.  Can either Gaussian or 
Hyperchem do this?  Or does other software exist that has this capability?

I apologize for my ignorance, but I have needed needed this kind of 
information in my own work.

Ray

Ray Fort Jr.			Voice: (207)-581-1180
Department of Chemistry	FAX:   (207)-581-1191
University of Maine		E-mail: rcfort@maine.edu
Orono, ME 04469		Web: chemistry.umeche.maine.edu/fort.html

Molecular modeling of organic and biomolecules; wood and paper chemistry

	


From chemistry-request@server.ccl.net Fri Dec 14 14:14:29 2001
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Date: Fri, 14 Dec 2001 11:14:07 -0800
To: chemistry@ccl.net
From: Eric Scerri <scerri@chem.ucla.edu>
Subject: quote from Bohr etc.
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

  My all time favorite quote is actually from Niels Bohr, I think:
>
>  "Prediction is very difficult... especially about the future."

This is a quotation from the Danish humorist and cartoonist Robert
Storm Petersen, known as "Storm P". Niels Bohr was probably fond of
it!

http://www.rene.belso.dk/StormP1.html

Yours, Jens >--<

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

Actually there is a serious aspect to Bohr's statement.

As we all know prediction can be used in the sense of retro-diction 
or genuine prediction (ie about the future).  There is a large 
literature in philosophy of science about the relative virtue of 
these two form of 'prediction' and the extent to which they each 
influence the acceptance of scientific theories.

The periodic table, although not exactly a "theory" has been the 
subject of part of this debate.
Was the periodic table accepted by the scientific community because 
of its dramatic predictions (Ge, Ga, Sc) or because it explained what 
was already known (the accommodation of all or most of the other then 
known elements).  Turns out it is not as clear-cut as histories 
usually state.  Even in the classic case of the periodic table 
genuine prediction of the future was not necessarily the most 
important factor in the acceptance of the system.

I could provide references if anybody is interested.

eric scerri



-- 

Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.wkap.nl/journalhome.htm/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html

From chemistry-request@server.ccl.net Fri Dec 14 11:38:33 2001
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From: "Danilo Gonzalez" <fgonzale@lauca.usach.cl>
To: <chemistry@ccl.net>
Subject: hbuild CHARMM
Date: Fri, 14 Dec 2001 13:35:00 -0300
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------=_NextPart_000_0023_01C184A4.2208F580
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	charset="Windows-1252"
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Hi all!,
I=92m a new user of CHARMM. When I try to put the H to my protein I have
the following error:
=20
***** Message from SEQRDR ***** THE SYSTEM CONTAINS132 TITRATABLE GROUPS
 THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE
AND RTF
 HIS - 16  ASP - 27  GLU - 36  LYS - 31  TYR - 22
=20
 CHARMM>
*****************************************************************
How can I fix this problem?
=20
Thanks a lot for any help=85
=20
Danilo Gonzalez-Nilo
=20
University of Santiago of Chile
Faculty of Chemistry and Biology
Casilla 40, Correo 33,
Santiago - Chile.
=20

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<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Hi all<span =
class=3DGramE>!,</span><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I=92m a new user of CHARMM. When I try to put the H =
to
my protein I have the following error:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>***** Message from SEQRDR ***** THE SYSTEM =
CONTAINS132
TITRATABLE GROUPS<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'>&nbsp;</span>THE =
USER MUST
PREDETERMINE THE </span></font><st1:place><st1:PlaceName><font size=3D2
  face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>PROTONATION</span></font></s=
t1:PlaceName><font
 size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =
</span></font><st1:PlaceType><font
  size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>STATE</span></font></st1:Pla=
ceType></st1:place><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> THROUGH THE
SEQUENCE AND RTF<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'>&nbsp;</span>HIS - =
<span
class=3DGramE>16<span style=3D'mso-spacerun:yes'>&nbsp; =
</span>ASP</span> - 27<span
style=3D'mso-spacerun:yes'>&nbsp; </span>GLU - 36<span
style=3D'mso-spacerun:yes'>&nbsp; </span></span></font><st1:place><font =
size=3D2
 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>LYS</span></font></st1:place=
><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> - 31<span
style=3D'mso-spacerun:yes'>&nbsp; </span>TYR - =
22<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span =
style=3D'mso-spacerun:yes'>&nbsp;</span>CHARMM&gt;<o:p></o:p></span></fon=
t></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>******************************************************=
***********<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>How can I fix this =
problem?<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Thanks a lot for any =
help=85<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoAutoSig><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;mso-no-proof:yes'>Danilo =
Gonzalez-Nilo<o:p></o:p></span></font></p>

<p class=3DMsoAutoSig><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;mso-no-proof:yes'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoAutoSig><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;mso-no-proof:yes'>University of Santiago of =
Chile<o:p></o:p></span></font></p>

<p class=3DMsoAutoSig><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;mso-no-proof:yes'>Faculty of Chemistry and =
Biology<o:p></o:p></span></font></p>

<p class=3DMsoAutoSig><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;mso-no-proof:yes'>Casilla 40, Correo =
33,<o:p></o:p></span></font></p>

<p class=3DMsoAutoSig><st1:City><st1:place><font size=3D3 face=3D"Times =
New Roman"><span
  =
style=3D'font-size:12.0pt;mso-no-proof:yes'>Santiago</span></font></st1:p=
lace></st1:City><span
style=3D'mso-no-proof:yes'> - =
</span><st1:country-region><st1:place><span
  =
style=3D'mso-no-proof:yes'>Chile</span></st1:place></st1:country-region><=
span
style=3D'mso-no-proof:yes'>.<o:p></o:p></span></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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From chemistry-request@server.ccl.net Fri Dec 14 15:13:44 2001
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Date: Fri, 14 Dec 2001 15:13:16 -0500 (EST)
From: "Robert Q. Topper" <topper@cooper.edu>
To: chemistry@ccl.net
Cc: TOPPER ROBERT <topper@cooper.edu>
Subject: ECCC8 January 18 deadline: Call for Papers
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ECCC8 Reminder of January 18 Deadline for Abstracts

Dear colleagues,

This is to remind you that abstracts for ECCC8,
the Eighth Electronic Computational Chemistry Conference,
are due by January 18, 2002 at http://eccc8.cooper.edu . 

Free online registration is now open 
and abstracts may be submitted online after registration.

As in previous years, the conference is multidisciplinary and
covers all aspects of computational and theoretical chemistry,
as well as computational molecular biology, computational
and theoretical molecular and atomic physics, visualization,
cheminformatics and the history of computational chemistry.
Participants will be able to view the presentations and discuss them
entirely through a web browser. As with the previous seven ECCCs,
ECCC8 has NO registration fee and is a completely virtual, online
conference.

Abstracts for all contributions to ECCC8 will be reviewed by the
Scientific Organizing Committee to insure novelty, scientific
value, and appopriateness for inclusion in the conference.

Presentations must be made in HTML format, and ideally
will take full advantage of the interactive nature of the
World-Wide Web to present their findings and conclusions.
In addition to completed work, work in progress is also acceptable for
an ECCC8 presentation. Authors may choose to either serve their
contributions from their own local web site, or may request us to upload
them to the ECCC8 server. Uploaded contributions will be removed from the
ECCC8 server at the end of ECCC8.

All authors are additionally encouraged to submit their work
for peer review and subsequent publication in the ECCC8
Proceedings. Current plans call for the Proceedings to be
published in Theoretical Chemistry Accounts, with the 
accompanying presentations permanently archived on 
TCA's web site. This peer review will be separate from, and in addition
to, the review of abstracts for the presentations. Detailed general
information on Theoretical Chemistry Accounts can be
found at the TCA web site:
http://link.springer.de/link/service/journals/00214/index.htm

As in ECCC7, a single weeklong "interactive" session will be part of the
conference. This session will be held via asynchronous postings of 
questions to the conference site, which authors can choose to receive
either at the site, at their personal email account, or both. All authors
must commit to having at least one co-author available 
(i.e. checking the discussion board at least daily) during the
"interactive" session to provide timely responses (within approximately 
24 hours) to any questions that conferees may have about their online 
presentation. Failure to participate fully in the interactive session may
result in a presentation being withdrawn from the conference.

Important dates for ECCC8 are:

         November  9, 2001 - Registration opens; call for papers
         January  18, 2002 - Abstracts due
         February 27, 2002 - Final online presentations due 
         March     4, 2002 - Conference begins
         March    18, 2002 - Interactive Session begins
         March    24, 2002 - Interactive Session ends
         April     1, 2002 - ECCC8 ends
         April    30, 2002 - Contributions to proceedings due from authors

Please note that presentations which are not completely 
ready by the beginning of the conference may be considered
to be withdrawn.

Complete details on how the conference will operate, abstract submission,
and conference registration will be found at

http://eccc8.cooper.edu

We invite all interested parties to contribute to ECCC8
and participate. Please share this announcement with
your colleagues and post it wherever appropriate so that
ECCC can continue to thrive and be a vital meeting for
the international computational chemistry community. 
ECCC cannot, and will not, continue without your active participation.

Please feel free to email me at topper@cooper.edu 
with your questions or comments.

Robert Q. Topper
Department of Chemistry
School of Engineering
The Cooper Union for the Advancement of Science and Art
51 Astor Place
New York, NY 10003







From chemistry-request@server.ccl.net Fri Dec 14 13:49:51 2001
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Message-ID: <006201c184d0$02ade7a0$33e46b8f@if.sc.usp.br>
From: "Alexandre Suman de Araujo" <asaraujo@if.sc.usp.br>
To: <chemistry@ccl.net>
Subject: Molecular Dynamics with small organometallics moelcules - Which is the best program?
Date: Fri, 14 Dec 2001 16:49:07 -0200
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Hi Guy!!!

I'm from Brazil and I'm starting my Phd where I'll develop studies of
Molecular Dynamics in small organometallics molecules. I studied the =
subject
a little, read some papers and looked for good programs to perform the
simulations. I found GROMACS and a friend of mine who study md for =
proteins
told me it'is a good choice.
I installed it and read some parts of manual and I saw it's developed =
mainly
for proteins. I tried to search for another program, I found a lot but =
in anyone the informatios are clearly. Them I'd like to ask you: Which =
is the best program to perform Molecular Dynamics simulations with small =
organometallics molecules???=20
Thank's a lot!!

Alexandre Suman de Araujo
IFSC - USP - S=E3o Carlos
UIN: 6194055

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<DIV><FONT face=3DArial size=3D2>Hi Guy!!!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV>I'm from Brazil and I'm starting my Phd where I'll develop studies=20
of<BR>Molecular Dynamics in small organometallics molecules. I studied =
the=20
subject<BR>a little, read some papers and looked for good programs to =
perform=20
the<BR>simulations. I found GROMACS and a friend of mine who study md =
for=20
proteins<BR>told me it'is a good choice.<BR>I installed it and read some =
parts=20
of manual and I saw it's developed mainly<BR>for proteins. I tried to =
search for=20
another program, I found a lot but in anyone the informatios are =
clearly. Them=20
I'd like to ask you: Which is the best program to perform Molecular =
Dynamics=20
simulations with small organometallics molecules??? </DIV>
<DIV>Thank's a lot!!<BR></DIV>
<DIV><FONT face=3DArial size=3D2>Alexandre Suman de Araujo<BR>IFSC - USP =
- S=E3o=20
Carlos<BR>UIN: 6194055</FONT></DIV></BODY></HTML>

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