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From: Philip Bays <pbays~at~saintmarys.edu>
Subject: Re: CCL:nanomathematics
Date: Wed, 8 Dec 2004 05:43:55 -0500
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All right -- someone else did it so I will follow :-)

Nanomathematics is the math of small numbers;

or

a nanomathematics course is a one offered in the math department that 
contains "little mathematics", one many of my students would sign up 
for in a flash.


On Dec 7, 2004, at 2:11 PM, Shobe, David wrote:

> I've never seen the term before, but logically it should refer to 
> arithmetic in which all numbers are rounded off to the nearest 
> billionth.  :-)


J. Philip Bays
Professor of Chemistry
Science Hall 158
Saint Mary's College
Notre Dame  IN  46556
(574) 284-4663

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All right -- someone else did it so I will follow :-)


Nanomathematics is the math of small numbers;


or


a nanomathematics course is a one offered in the math department that
contains "little mathematics", one many of my students would sign up
for in a flash.



On Dec 7, 2004, at 2:11 PM, Shobe, David wrote:


<excerpt>I've never seen the term before, but logically it should
refer to arithmetic in which all numbers are rounded off to the
nearest billionth.  :-)

</excerpt>


<smaller>J. Philip Bays

Professor of Chemistry

Science Hall 158

Saint Mary's College

Notre Dame  IN  46556

(574) 284-4663</smaller>


--Apple-Mail-6--358616094--



From chemistry-request@ccl.net Tue Dec  7 23:13:08 2004
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Subject: CCG Excellence Award Winners
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Dear Computational Chemistry Community,

It is my pleasure on behalf of the ACS Division of Computers in 
Chemistry to announce the winners of the Chemical Computing Group CCG 
Excellence Spring 2005 ACS San Diego ACS meeting.  They are:

=====================

Anastassia Alexandrova  - Department of Chemistry, Utah State University 
"Ab Initio Genetic Algorithm-based Elucidation of Multiply Aromatic 
Clusters" (Alexander I. Boldyrev)

Biggi Albrecht  - Unilever Center for Molecular Informatics, Cambridge 
University "Uncovering Networks within Protein Structure" (Guy H. Grant)

Dechuan Zhuang  - Department of Chemistry, RPI "Consensus Descriptor 
Selection under Multiple Objectives using Linear Support Vector 
Regression" (Curt M. Breneman)

Hanbin Liu - Department of Chemistry, University of Pittsburgh "On the 
Convergence of a Hybrid Parallel Tempering Tsallis Statistics Monte 
Carlo Algorithm" (Ken Jordan)

John Mongan - Department of Chemistry, University of California, San 
Diego "Discrete State Constant pH Molecular Dynamics in Generalized Born 
Implicit Solvent" (J. Andrew McCammon)

Matt Sundling - Department of Chemistry, RPI "PEST vs CoMFA:  A 
Comparative Study of two 3D QSAR Technologies" (Curt M .Breneman)

Melinda Harrison  - Department of Chemistry, Duquesne University "A 
QM/MM' Approach  to Modeling  the Zn(II)/Cu(I) Core of a Protein" (Jeff 
Evanseck)

Scott Yockel - Department of Chemistry, University of North Texas, 
Denton "Structures and Energetics of Small Third-Row Molecules with 
Correlation-Consistent Basis Sets" (Angela Wilson)

Xianlong Vincent Wang - Department of Chemistry, Bryn Mawr College "Ab 
Initio Studies of Methyl and t-Butyl Group Internal Rotation in 
Aromatic  Molecular Crystals" (Frank Mallory)

Zunnan Huang - Department of Chemistry, University of Oklahoma 
"Trajectory-randomized Replica Canonical and Microcanonical Ensembles 
Simulations and Limitations of MD simulations" (Ralph Wheeler)

 
Congratulations to the winners!!  We look forward to seeing their talks 
and posters at the ACS Meeting in San Diego, California next Spring.



--------------080009080503050101010802
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Dear Computational Chemistry Community,<br>
<br>
It is my pleasure on behalf of the ACS Division of Computers in
Chemistry to announce the winners of the Chemical Computing Group CCG
Excellence Spring 2005 ACS San Diego ACS meeting.&nbsp; They are:<br>
<br>
<p class="MsoNormal">=====================<o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal" style=""><span lang="IT" style="">Anastassia
Alexandrova&nbsp; - Department
of Chemistry, Utah State University &#8220;Ab Initio Genetic Algorithm-based
Elucidation of Multiply Aromatic Clusters&#8221; (</span>Alexander I.
Boldyrev)<o:p></o:p></p>
<p class="MsoNormal" style=""><span lang="IT" style="">Biggi Albrecht <span
 style="">&nbsp;</span>- Unilever Center for Molecular Informatics,
Cambridge University &#8220;Uncovering Networks within Protein Structure&#8221;
(Guy H.
Grant)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="IT" style="">Dechuan Zhuang<span
 style="">&nbsp; </span>- Department of Chemistry, RPI &#8220;Consensus
Descriptor Selection under Multiple Objectives using Linear Support
Vector
Regression&#8221; (Curt M. Breneman)</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span lang="IT" style="">Hanbin Liu &#8211;
Department of Chemistry,
University of Pittsburgh &#8220;</span>On the Convergence of a Hybrid
Parallel
Tempering Tsallis Statistics Monte Carlo Algorithm<span lang="IT"
 style="">&#8221; (Ken Jordan)</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span lang="IT" style="">John Mongan &#8211;
Department of Chemistry,
University of California, San Diego &#8220;Discrete State Constant pH
Molecular
Dynamics in Generalized Born Implicit Solvent&#8221; (J. Andrew McCammon)</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span lang="SV" style="">Matt Sundling &#8211;
Department of Chemistry,
RPI &#8221;PEST vs CoMFA:<span style="">&nbsp; </span>A Comparative Study
of two 3D QSAR Technologies&#8221; (Curt M .Breneman)</span><o:p></o:p></p>
<p class="MsoNormal" style=""><span lang="SV" style="">Melinda Harrison
<span style="">&nbsp;</span>- Department of Chemistry, Duquesne University
&#8221;A QM/MM&#8217; Approach<span style="">&nbsp; </span>to Modeling<span style="">&nbsp; </span>the
Zn(II)/Cu(I) Core of a Protein&#8221; (Jeff
Evanseck)</span><o:p></o:p></p>
<p class="MsoNormal" style="">Scott
Yockel &#8211; Department of Chemistry, <st1:place><st1:PlaceType>University</st1:PlaceType>
of <st1:PlaceName>North Texas</st1:PlaceName></st1:place>, <st1:City><st1:place>Denton</st1:place></st1:City>
&#8220;Structures and Energetics of Small Third-Row Molecules with
Correlation-Consistent Basis Sets&#8221; (Angela Wilson)<o:p></o:p></p>
<p class="MsoNormal" style="">Xianlong
Vincent Wang &#8211; Department of Chemistry, <st1:place><st1:PlaceName>Bryn</st1:PlaceName>
<st1:PlaceName>Mawr</st1:PlaceName> <st1:PlaceType>College</st1:PlaceType></st1:place>
&#8220;Ab Initio Studies of Methyl and t-Butyl Group Internal Rotation in
Aromatic<span style="">&nbsp; </span>Molecular <st1:City><st1:place>Crystals</st1:place></st1:City>&#8221;
(Frank Mallory)<o:p></o:p></p>
<p class="MsoNormal" style="">Zunnan
Huang &#8211; Department of Chemistry, University of <st1:State><st1:place>Oklahoma</st1:place></st1:State>
&#8220;Trajectory-randomized Replica Canonical and Microcanonical Ensembles
Simulations and Limitations of MD simulations&#8221; (Ralph Wheeler)<o:p></o:p></p>
<p class="MsoNormal"><o:p>&nbsp;<br>
Congratulations to the winners!!&nbsp; We look forward to seeing their talks
and posters at the ACS Meeting in San Diego, California next Spring.<br>
</o:p></p>
<p class="MsoNormal"><o:p><br>
</o:p></p>
</body>
</html>

--------------080009080503050101010802--



From chemistry-request@ccl.net Wed Dec  8 06:46:53 2004
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From: Arvydas Tamulis <tamulis:at:mserv.itpa.lt>
To: "Shobe, David" <dshobe:at:sud-chemieinc.com>
cc: Chungen Liu <cgliu:at:netra.nju.edu.cn>,
   Vykintas Tamulis <vykintas:at:mserv.itpa.lt>, chemistry:at:ccl.net
Subject: Re: CCL:nanomathematics
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I think nanomathematics should describe processes in quantum nanophysics: 
quantum statistics, quantum noises. Very important is that quantum logics 
possesses more logic functions (gates) in comparison with classical 
Boolean logics.

Regards,
Arvydas Tamulis
www.itpa.lt/~tamulis/

On Tue, 7 Dec 2004, Shobe, David wrote:

> I've never seen the term before, but logically it should refer to arithmetic in which all numbers are rounded off to the nearest billionth.  :-)
>
> --David Shobe, Ph.D., M.L.S.
> S|d-Chemie, Inc.
> phone (502) 634-7409
> fax (502) 634-7724
>
> Don't bother flaming me: I'm behind a firewall.
>
>
> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request:at:ccl.net]On
> Behalf Of Chungen Liu
> Sent: Monday, December 06, 2004 7:44 PM
> To: chemistry:at:ccl.net
> Subject: CCL:nanomathematics
>
>
> Hi, all,
>
> Would anyone give a description about the concept "nanomathematics"?
>
>
> Thanks in advance.
>
> Chungen
>
>
>
>
>
>
>
>
>
>
>
>
> -= This is automatically added to each message by the mailing script =-
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From chemistry-request@ccl.net Wed Dec  8 10:47:08 2004
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Date: Wed, 8 Dec 2004 18:02:21 +0200 (EET)
From: Arvydas Tamulis <tamulis:at:mserv.itpa.lt>
To: chemistry:at:ccl.net
Subject: Quantum yield of photochemical reactions
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Dear Colleagues,

Would you please to say how to calculate quantum yield of photochemical 
reactions using resulting files of Gaussian03 or GAMESS-US calculations.
Or maybe you can offer other possible evaluations of quantum yield of 
photochemical reactions.

Best regards,
Arvydas Tamulis
www.itpa.lt/~tamulis/



From chemistry-request@ccl.net Wed Dec  8 13:51:29 2004
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Date: Wed, 08 Dec 2004 14:06:21 -0500
From: Kadir Diri <kadir~at~visual1.chem.pitt.edu>
Subject: Re: CCL:Computation Resource Requirement.
In-reply-to: <41B5CEE1.10203~at~ndsu.nodak.edu>
To: Pijush Ghosh <pijush.ghosh~at~ndsu.nodak.edu>
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Hi! What you can do to get an idea about the timings on a single cpu is 
the following: do a smaller calculation (smaller basis set and/or 
smaller molecule). Then scale the timings accordingly for larger basis 
sets and more atoms. In Hartree-Fock, the 2 electron integrals will 
scale as N^4 but the integral transformation will scale as N^5.
As to the case with multiple CPU`s, it depends on many factors, for 
example on how good the code that you use is. Also, the speed will vary 
> from one architecture to another. It is also important how the code 
works, i.e. whether it uses shared memory on a multiple cpu machine or 
whether it runs across many nodes. There are probably many other 
factors, like the speed and the configuration of the network, so it is 
not very easy to answer that part of your question, but you will be able 
to figure out the answer after a few test calculations.
kadir


Pijush Ghosh wrote:

> CCL Users,
>       being new to the field of computational quantum mechanics, i 
> have a basic question on the requirement of the resources for this 
> type of computation.  Can anybody  cite any reference where i can get 
> some relation between number of processors and time required  with 
> that of number of atoms in a system , basis set used, etc.
>     In my system of Hydroxyapatite- polymer I have the following details:
>
> atom                 number
>
> Calcium              20
> Phosphorous      12
> Oxygen              54
> Hydrogen           10
> Carbon                 3
>
>
> Basis set -            6-31+G**
> Method -              HF (Hartree Fock)
>
>
> can somebody  give idea on  processor-hour required. All my 
> simulations are run on NCSA machines.
>
>
> All suggesions and information appreciated in advance.
>
>
> Pijush Ghosh.
> NDSU.
>
>
>
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From chemistry-request@ccl.net Wed Dec  8 05:36:40 2004
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From: Eugen Leitl <eugen|at|leitl.org>
To: chemweb|at|ic.ac.uk, chemistry|at|ccl.net
Subject: [QSAR-devel] Chemical Semantic Web and Thanks (fwd from pm286|at|cam.ac.uk)
Message-ID: <20041208105152.GR9221|at|leitl.org>

----- Forwarded message from Peter Murray-Rust <pm286|at|cam.ac.uk> -----

From: Peter Murray-Rust <pm286|at|cam.ac.uk>
Date: Wed, 08 Dec 2004 09:50:16 +0000
To: JOELib devel <joelib-devel|at|lists.sourceforge.net>,
	JOELib help <joelib-help|at|lists.sourceforge.net>,
	cdk <cdk-devel|at|lists.sourceforge.net>,
	Octet Developer <octet-devel|at|lists.sourceforge.net>,
	QSAR Development <qsar-devel|at|lists.sourceforge.net>,
	OpenBabel-discuss|at|lists.sourceforge.net,
	Beda Kosata <beda|at|zirael.org>
Subject: [QSAR-devel] Chemical Semantic Web and Thanks
X-Mailer: QUALCOMM Windows Eudora Version 5.1.1

[Crossposted to several OpenSource lists - please reply thoughtfully. I 
will collate significant replies]

I presented an invited lecture at the Royal Soc Chem yesterday on "The 
Chemical Semantic Web" and highlighted the impressive contribution of the 
Open Source movement in chemistry. I hope I managed to acknowledge most 
people's contributions. It generated a lively discussion in which, I think, 
the Open Source approach came out very positively.

Two common negative questions were presented:

"Who pays for it"
 the implication was that if there was no commercial development the 
software was second-class and there was no future for it. My response was 
that the code would be eagerly adopted by the bioinformatics community 
(strongly confirmed by Mike Ashburner) and we are starting to set up strong 
links with the Bioinformatics community on small molecules. This question 
came from the pharma industry and so I challenged them to put something 
back into the communal process. It's noticeable that the pharma industry is 
a consumer of our efforts but has not contributed anything in return and 
continues to pay for overpriced software products that do not use modern 
methodology. (I spent 15 years in Glaxo so I feel I have a right to 
criticise the industry). I know that pharma industry reads this list and I 
would be delighted if there were some who wished to support communal 
activity. [I would suggest they mail me directly and I will summarise 
replies. All replies will be assumed to be Open unless specifically 
indicated]. One approach would be to support a physical workshop on 
chemical open source. Particular topics could be:
- markup languages
- communal chemical ontologies (e.g. descriptors)
- Open datasets
- use of InChI (we are very excited about this)
- graphical components
- common code libraries
- web services (I'll mail later)
The only contribution that I know of from the pharma industry to 
chemoinformatics is the JME editor which is free, but despite repeated 
requests is not Open and not likely to be. It could be withdrawn at any time.

"Open source is unfair to commercial developers"
I think this attitude is particularly strong in the US and perhaps Germany. 
The idea is that public funding should not be used to compete against 
commercial organisations. As Mike Ashburner replied, most Open software in 
bioinformatics is written by people on short term contracts often with no 
possibility of extension. I know that made contributors to these lists do 
not have jobs. I developed much of CML when I was unemployed after being 
made redundant from Glaxo.
I would be more (slightly) more sympathetic to this view if the chemical 
software industry provided anything substantial to the community. I know of 
no support for Open efforts from the chemical software industry other than
a very undersupported effort to get an Open Management Group spec for 
chemistry. I was invited to contribute CML as the core of this spec, but 
even then it was made clear that I would not even have my (foreign) travel 
expenses paid - even though I had no job.
Note that "free" is not good enough and may even by counterproductive. 
Closed software often stifles development as there is no API and the 
software can be withdrawn at any time. That is why we are so keen to see a 
JChempaint component as a universal Open chemical editor for the web.

In fact I think the tide is turning. The components that you are all 
developing are ideal for Web Services, which will have the potential to 
rapidly become a major player in the chemoinformatics market. Between the 
members of this community we have standards, data, transformers, 
algorithms, repositories, query languages, graphics and much more. I'll put 
forward a strategy in the next mail(s).

Meanwhile - when you are hacking the latest set of bugs at 0200 in the 
morning, take heart - it really is appreciated - and yes - the day of Open 
Source for "chemistry" is dawning. In fact I think the centre of gravity of 
chemical software development is starting to shift towards bioscience [and 
materials] so that people will simply refer to the informatics of small 
molecules as "bioinformatics"



Best

P.

Many thanks to those who have sponsored our Open Source development: Royal 
Soc. Chemistry, Nature Publishing Group, Cyprotex. More about this later.


Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069



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From chemistry-request@ccl.net Wed Dec  8 13:56:48 2004
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Date: Wed, 08 Dec 2004 13:14:47 -0600
From: Pijush Ghosh <pijush.ghosh{at}ndsu.nodak.edu>
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To: Kadir Diri <kadir{at}visual1.chem.pitt.edu>
CC: CHEMISTRY{at}ccl.net
Subject: Re: CCL:Computation Resource Requirement.
References: <41B5CEE1.10203{at}ndsu.nodak.edu> <41B750AD.5080103{at}visual1.chem.pitt.edu>
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I thank you all for your valuable suggestions on my issue of 
coumputation resource requirement. I think they are of big help to me.

Pijush.

Kadir Diri wrote:

> Hi! What you can do to get an idea about the timings on a single cpu 
> is the following: do a smaller calculation (smaller basis set and/or 
> smaller molecule). Then scale the timings accordingly for larger basis 
> sets and more atoms. In Hartree-Fock, the 2 electron integrals will 
> scale as N^4 but the integral transformation will scale as N^5.
> As to the case with multiple CPU`s, it depends on many factors, for 
> example on how good the code that you use is. Also, the speed will 
> vary from one architecture to another. It is also important how the 
> code works, i.e. whether it uses shared memory on a multiple cpu 
> machine or whether it runs across many nodes. There are probably many 
> other factors, like the speed and the configuration of the network, so 
> it is not very easy to answer that part of your question, but you will 
> be able to figure out the answer after a few test calculations.
> kadir
>
>
> Pijush Ghosh wrote:
>
>> CCL Users,
>>       being new to the field of computational quantum mechanics, i 
>> have a basic question on the requirement of the resources for this 
>> type of computation.  Can anybody  cite any reference where i can get 
>> some relation between number of processors and time required  with 
>> that of number of atoms in a system , basis set used, etc.
>>     In my system of Hydroxyapatite- polymer I have the following 
>> details:
>>
>> atom                 number
>>
>> Calcium              20
>> Phosphorous      12
>> Oxygen              54
>> Hydrogen           10
>> Carbon                 3
>>
>>
>> Basis set -            6-31+G**
>> Method -              HF (Hartree Fock)
>>
>>
>> can somebody  give idea on  processor-hour required. All my 
>> simulations are run on NCSA machines.
>>
>>
>> All suggesions and information appreciated in advance.
>>
>>
>> Pijush Ghosh.
>> NDSU.
>>
>>
>>
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>
>




From chemistry-request@ccl.net Wed Dec  8 15:14:05 2004
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To: chemistry_at_ccl.net
From: Geoff Hutchison <grh25_at_cornell.edu>
Subject: Gaussian PBC input files?
Date: Wed, 8 Dec 2004 15:29:15 -0500
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I've been trying to run PBC calculations with g03 unsuccessfully. (I'm 
currently trying g03 C.02, but have tried older versions too.) This is 
running on a Linux box, and runs other Gaussian jobs just fine.

Here's my test file -- it's for graphite, and was quite literally 
copied out of the G03 manual. (I figured I was having problems with 
input in *my* files first, so I decided to try theirs...)

---- graphite.com
#n HF/6-31+G* SCF=Tight PBC(NKPoint=48,CellRange=20)

  graphite

0  1
C                   0.000000    0.000000    0.000000
C                   0.000000    1.429118    0.000000
TV                  2.475315    0.000000    0.000000
TV                 -1.219952    2.133447    0.000000
----

In return, I get: (lots of stuff, and carbon coordinates) ...
  TV                    2.47532   0.        0.
  TV                   -1.21995   2.13345   0.
  End of file in ZSymb.
  Error termination via Lnk1e in /usr/local/g03/l101.exe at Wed Dec  8 
15:22:53
  2004.

Any help or suggestions would be greatly appreciated. Thanks in advance!
-Geoff

--
-Dr. Geoffrey Hutchison		<grh25_at_cornell.edu>
Abruqa Group, Molelectronics	(607) 255-7568
Cornell Chemistry			http://abruna.chem.cornell.edu/