From owner-chemistry@ccl.net Tue Oct 11 02:42:00 2005
From: "Goedele Roos groos]~[vub.ac.be" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: Condensed Fukui Functions
Message-Id: <-29535-051011021526-31903-KuhEjaYj32HnfSd5p9qGfQ!=!server.ccl.net>
X-Original-From: Goedele Roos <groos(a)vub.ac.be>
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Date: Tue, 11 Oct 2005 08:15:20 +0200 (MEST)
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Sent to CCL by: Goedele Roos [groos[A]vub.ac.be]
Maybe you  can use an other descriptor like local softness to predict the reactivity. Or even better apply the HSAB principle, formulated by Pearson.
You can read my paper: Roos et al, J. Phys Chem A, 2003, 107, 6828.
I use the NPA population analysis.


>Dear CCLers,
>We have some problems in the prediction of reactivity when we calculate condensed Fukui functions with the finite difference approximation using N, N-1 and N+1 systems. 
>In your opinion, what is the best method for the calculation of these indexes ?
>Which population analysis do you suggest ?
>Sincerely
>
>
>		
>---------------------------------
> Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger
> Téléchargez le ici !  
>

Drs. Goedele Roos
Dienst Algemene Chemie (ALGC)
Vrije Universiteit Brussel (VUB)
Pleinlaan 2
B-1050 Brussels
Tel: 0032-2-629 35 16
Fax: 0032-2-629 33 17


From owner-chemistry@ccl.net Tue Oct 11 03:17:01 2005
From: "Marcel Swart m.swart],[few.vu.nl" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: constrained geometry optmisation of molecular complexes
Message-Id: <-29536-051011023030-669-DvEGgJYaFwvd93ROUU44Vw-,-server.ccl.net>
X-Original-From: Marcel Swart <m.swart|,|few.vu.nl>
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Date: Tue, 11 Oct 2005 08:29:22 +0200
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Sent to CCL by: Marcel Swart [m.swart^-^few.vu.nl]

--Apple-Mail-1-381106842
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=WINDOWS-1252;
	format=flowed

On Oct 10, 2005, at 6:29 PM, James Kirkpatrick james.kirkpatrick ..=20
imperial.ac.uk wrote:

> I wish to perform geometry calculations on two of molecules, each=20
> molecule contains rougly 20 heavy atoms. So far as I understand, HF=20
> methods, semi-empirical methods and most DFT functionals will not=20
> describe van-der-Waals forces (responsible for a good part of the=20
> non-binding interaction?) correctly.

Wrong.
Some DFT methods do not describe dispersion correctly,
but many do give the correct description for hydrogen-bonds,
see Fonseca Guerra, C.; Bickelhaupt, F.M.; Snijders, J.G.; Baerends,=20
E.J.
  Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and=20
Experiment
J. Am. Chem. Soc.=A0 2000,  122, 4117-4128
and give also the favorable dispersive forces, see
Xu, Goddard III, PNAS 101 (2004) 2673

PW91 or PBE are functionals that you might want to consider using,
especially because they were based on non-empirical grounds.

Another issue would be pi-pi stacking, which remains a problematic=20
interaction;
MP2 can also not be trusted, it overestimates the interaction; CCSD(T)=20=

seems
to be warranted, but it can not yet be used on larger systems=20
unfortunately.

=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96
dr. Marcel Swart

Theoretische Chemie
Vrije Universiteit Amsterdam
Faculteit der Exacte Wetenschappen

De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

Tel		+31-(0)20-5987619
Fax		+31-(0)20-5987629
E-mail	m.swart#,#few.vu.nl
Web		http://www.few.vu.nl/~swart
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96


--Apple-Mail-1-381106842
Content-Transfer-Encoding: quoted-printable
Content-Type: text/enriched;
	charset=WINDOWS-1252

On Oct 10, 2005, at 6:29 PM, James Kirkpatrick james.kirkpatrick ..
imperial.ac.uk wrote:


<excerpt>I wish to perform geometry calculations on two of molecules,
each molecule contains rougly 20 heavy atoms. So far as I understand,
HF methods, semi-empirical methods and most DFT functionals will not
describe van-der-Waals forces (responsible for a good part of the
non-binding interaction?) correctly.

</excerpt>

Wrong.

Some DFT methods do not describe dispersion correctly,

but many do give the correct description for hydrogen-bonds,

<italic><color><param>FFFF,0000,0000</param>see Fonseca Guerra, C.;
Bickelhaupt, F.M.; Snijders, J.G.; Baerends, E.J.=20

 Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and
Experiment=20

J. Am. Chem. Soc.=A0 2000,  122, 4117-4128

</color></italic>and give also the favorable dispersive forces, see

<italic><color><param>FFFF,0000,0000</param>Xu, Goddard III, PNAS 101
(2004) 2673

</color></italic>

PW91 or PBE are functionals that you might want to consider using,

especially because they were based on non-empirical grounds.


Another issue would be pi-pi stacking, which remains a problematic
interaction;

MP2 can also not be trusted, it overestimates the interaction; CCSD(T)
seems

to be warranted, but it can not yet be used on larger systems
unfortunately.


=
<fontfamily><param>Helvetica</param><x-tad-smaller>=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96

=
</x-tad-smaller></fontfamily><fontfamily><param>Papyrus</param><x-tad-bigg=
er>dr.
Marcel Swart

=
</x-tad-bigger></fontfamily><fontfamily><param>Papyrus</param><x-tad-small=
er>

=
</x-tad-smaller></fontfamily><fontfamily><param>Osaka</param><x-tad-smalle=
r>Theoretische
Chemie

Vrije Universiteit Amsterdam

Faculteit der Exacte Wetenschappen


De Boelelaan 1083

1081 HV Amsterdam

The Netherlands


Tel		+31-(0)20-5987619

Fax		+31-(0)20-5987629

E-mail	m.swart#,#few.vu.nl

Web		http://www.few.vu.nl/~swart

=
</x-tad-smaller></fontfamily><fontfamily><param>Helvetica</param><x-tad-sm=
aller>=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96

</x-tad-smaller></fontfamily>


--Apple-Mail-1-381106842--


From owner-chemistry@ccl.net Tue Oct 11 08:27:00 2005
From: "Noel O Boyle no228 ~~ cam.ac.uk" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Where can you publish articles on software?
Message-Id: <-29537-051011053401-1507-rGpBYstNKShNqp4m6kf/3Q(_)server.ccl.net>
X-Original-From: "Noel O'Boyle" <no228[a]cam.ac.uk>
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Date: Tue, 11 Oct 2005 09:45:01 +0100
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Sent to CCL by: "Noel O'Boyle" [no228]_[cam.ac.uk]
Dear CCLers,

Where can one publish articles on programs that are of general interest
to computational chemists, but which do not contain new algorithms?

For example, I have a program that parses the output of the logfiles of
certain computational chemistry programs, shows the progress of the
calculation graphically and can convolute some spectra. I would say that
this is of general interest (judging by the number of downloads), but I
cannot figure out whether any journals would accept an article
describing the software (which is freely available, and open source).

Regards,
Noel O'Boyle.
(http://gausssum.sf.net is the program in question)


From owner-chemistry@ccl.net Tue Oct 11 10:06:00 2005
From: "Konrad Hinsen khinsen#,#cea.fr" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: W:CCL: Where can you publish articles on software?
Message-Id: <-29538-051011095957-10349-kF0PI3aoBlGLXhmT/NrpHA-$-server.ccl.net>
X-Original-From: "Konrad  Hinsen" <khinsen{:}cea.fr>


Sent to CCL by: "Konrad  Hinsen" [khinsen(-)cea.fr]
On Oct 11, 2005, at 10:45, Noel O Boyle no228 ~~ cam.ac.uk wrote:

> Where can one publish articles on programs that are of general interest
> to computational chemists, but which do not contain new algorithms?

The Journal of Computational Chemistry has a section for articles describing programs, but I don't 
know what their criteria for acceptance are.

There is also Computer Physics Communications, which has some chemistry-oriented contributions in 
spite of "physics" in the title.

---------------------------------------------------------------------
Konrad Hinsen
Laboratoire Lon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen[*]cea.fr
---------------------------------------------------------------------


From owner-chemistry@ccl.net Tue Oct 11 10:40:01 2005
From: "Michel Petitjean ptitjean-.-itodys.jussieu.fr" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Re: Where can you publish articles on software?
Message-Id: <-29539-051011102337-14464-iJRNte2HhoJXWUgsgC0Luw(-)server.ccl.net>
X-Original-From: Michel Petitjean <ptitjean-*-itodys.jussieu.fr>
Date: Tue, 11 Oct 2005 16:23:29 +0200 (MEST)


Sent to CCL by: Michel Petitjean [ptitjean . itodys.jussieu.fr]
To: chemistry[]ccl.net
Subject: CCL: Re: Where can you publish articles on software?

This programme is surely useful, but the editors of research journals
would probably not accept it for publication. If this kind of article
is acceptable, I guess that many people would produce tons of technical
programmes and have hundreds of papers in their CV, then apply for
some full Professor position without having done any scientific research.

Publishing programmes for computational chemistry (or other) means
(a) creating an original algorithm, and (b) programming it, and (c)
running it on suitable data of interest.

Regrettably, numerous molecular modeling papers published on the basis
of step (c) alone bear the same value that papers involving (a)+(b)+(c).

Michel Petitjean,                     Email: petitjean[]itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean[]ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

Sent to CCL by: "Noel O'Boyle" [no228]_[cam.ac.uk]:
> Dear CCLers,
>
> Where can one publish articles on programs that are of general interest
> to computational chemists, but which do not contain new algorithms?
>
> For example, I have a program that parses the output of the logfiles of
> certain computational chemistry programs, shows the progress of the
> calculation graphically and can convolute some spectra. I would say that
> this is of general interest (judging by the number of downloads), but I
> cannot figure out whether any journals would accept an article
> describing the software (which is freely available, and open source).
>
> Regards,
> Noel O'Boyle.
> (http://gausssum.sf.net is the program in question)


From owner-chemistry@ccl.net Tue Oct 11 11:38:01 2005
From: "Sergio Emanuel Galembeck segalemb+/-usp.br" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: Where can you publish articles on software?
Message-Id: <-29540-051011103933-19874-ER9G9ashbXn6BfcG9VDfmg:-:server.ccl.net>
X-Original-From: Sergio Emanuel Galembeck <segalemb\a/usp.br>
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Date: Tue, 11 Oct 2005 10:37:24 -0300
MIME-Version: 1.0


Sent to CCL by: Sergio Emanuel Galembeck [segalemb%%usp.br]
Noel,

   I suggest Journal of Computational Chemistry.

              Best regards,

                       Sergio

==============================================================
Sergio Emanuel Galembeck
Assistant Professor in Physical Chemistry
Departamento de Quimica
Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto
Universidade de Sao Paulo
Av Bandeirantes, 3900
Ribeirao Preto, SP
Brasil

phone: +55-16-602-37-65
fax: +55-16-633-81-51
e-mail: segalemb AT usp.br
==============================================================


Citando "Noel O Boyle no228 ~~ cam.ac.uk" <owner-chemistry.:-:.ccl.net>:

> 
> Sent to CCL by: "Noel O'Boyle" [no228]_[cam.ac.uk]
> Dear CCLers,
> 
> Where can one publish articles on programs that are of general interest
> to computational chemists, but which do not contain new algorithms?
> 
> For example, I have a program that parses the output of the logfiles of
> certain computational chemistry programs, shows the progress of the
> calculation graphically and can convolute some spectra. I would say that
> this is of general interest (judging by the number of downloads), but I
> cannot figure out whether any journals would accept an article
> describing the software (which is freely available, and open source).
> 
> Regards,
> Noel O'Boyle.
> (http://gausssum.sf.net is the program in question)> 
> 
> 
>


From owner-chemistry@ccl.net Tue Oct 11 12:13:00 2005
From: "David van der Spoel spoel{:}xray.bmc.uu.se" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Where can you publish articles on software?
Message-Id: <-29541-051011102449-14749-8teP1pLOtMmKbNL5aCd0IA() server.ccl.net>
X-Original-From: David van der Spoel <spoel[A]xray.bmc.uu.se>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain
Date: Tue, 11 Oct 2005 15:35:16 +0200
Mime-Version: 1.0


Sent to CCL by: David van der Spoel [spoel_._xray.bmc.uu.se]
On Tue, 2005-10-11 at 09:45 +0100, Noel O Boyle no228 ~~ cam.ac.uk
wrote:
> Sent to CCL by: "Noel O'Boyle" [no228]_[cam.ac.uk]
> Dear CCLers,
> 
> Where can one publish articles on programs that are of general interest
> to computational chemists, but which do not contain new algorithms?
Comp. Phys. Comm. does that.

> 
> For example, I have a program that parses the output of the logfiles of
> certain computational chemistry programs, shows the progress of the
> calculation graphically and can convolute some spectra. I would say that
> this is of general interest (judging by the number of downloads), but I
> cannot figure out whether any journals would accept an article
> describing the software (which is freely available, and open source).
> 
> Regards,
> Noel O'Boyle.
> (http://gausssum.sf.net is the program in question)> 
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel- -xray.bmc.uu.se    spoel- -gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From owner-chemistry@ccl.net Tue Oct 11 12:47:01 2005
From: "George Fitzgerald gxf]-[accelrys.com" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: Condensed Fukui Functions
Message-Id: <-29542-051011114210-28874-SaYOmtiFoITEvETWnau7Gg::server.ccl.net>
X-Original-From: George Fitzgerald <gxf!^!accelrys.com>
Content-Type: multipart/alternative; boundary="=_alternative 00563FD588257097_="
Date: Tue, 11 Oct 2005 08:42:04 -0700
MIME-Version: 1.0


Sent to CCL by: George Fitzgerald [gxf ~ accelrys.com]
This is a multipart message in MIME format.
--=_alternative 00563FD588257097_=
Content-Type: text/plain; charset="US-ASCII"

In DMol3 I implemented Fukui indices using both Mulliken and Hirshfeld 
charges. The Hirshfeld are clearly more reasonable, as already pointed 
out.  Olah et al J Phys Chem A 106, 2885 (2002) calls these Stockholder 
charges and compares several different charges.

You don't say what sort of problems you're having. One thing I have not 
see addressed in the literature is the use of occupations besides N+1 and 
N-1. DFT is perfectly happy to run using fractional occupations. I usually 
do my Fukui analyses using delta-Q of 0.1 electron. One advantage is that 
this leads to faster scf convergence.

More importantly, the eigenvalues in DFT are the chemical potential 
defined by mu=dE/dN where N is electron occupation and E is total energy. 
If you evaluate mu by finite difference on N and compare to the SCF 
eigenvalue, you get around 100% error using N=1.0. You need N=0.01 to get 
agreement to a few %, but this obviously produces very small changes in 
density. My compromise is to use N=0.1. Do you think this would help your 
case?

george
____________________________________________
George Fitzgerald, Ph.D.       gxf[a]accelrys.com
Accelrys, Inc.                             Tel:  +1 858 799 5360
10188 Telesis Court                 Fax: +1 858 799 5100
Suite 100                                     Mobile: +1 858 692 8722
San Diego, CA 92121



"b wafaa wafaab2*_*yahoo.fr" <owner-chemistry[a]ccl.net> 
Sent by: owner-chemistry[a]ccl.net
10/10/2005 05:51 AM
Please respond to
"CCL Subscribers" <chemistry[a]ccl.net>


To
"Fitzgerald, George " <gxf[a]accelrys.com>
cc

Subject
CCL: Condensed Fukui Functions






Dear CCLers,
We have some problems in the prediction of reactivity when we calculate 
condensed Fukui functions with the finite difference approximation using 
N, N-1 and N+1 systems. 
In your opinion, what is the best method for the calculation of these 
indexes ?
Which population analysis do you suggest ?
Sincerely

--=_alternative 00563FD588257097_=
Content-Type: text/html; charset="US-ASCII"


<br><font size=2 face="sans-serif">In DMol3 I implemented Fukui indices
using both Mulliken and Hirshfeld charges. The Hirshfeld are clearly more
reasonable, as already pointed out. &nbsp;Olah et al J Phys Chem A 106,
2885 (2002) calls these Stockholder charges and compares several different
charges.</font>
<br>
<br><font size=2 face="sans-serif">You don't say what sort of problems
you're having. One thing I have not see addressed in the literature is
the use of occupations besides N+1 and N-1. DFT is perfectly happy to run
using fractional occupations. I usually do my Fukui analyses using delta-Q
of 0.1 electron. One advantage is that this leads to faster scf convergence.</font>
<br>
<br><font size=2 face="sans-serif">More importantly, the eigenvalues in
DFT are the chemical potential defined by mu=dE/dN where N is electron
occupation and E is total energy. If you evaluate mu by finite difference
on N and compare to the SCF eigenvalue, you get around 100% error using
N=1.0. You need N=0.01 to get agreement to a few %, but this obviously
produces very small changes in density. My compromise is to use N=0.1.
Do you think this would help your case?</font>
<br>
<br><font size=2 face="sans-serif">george</font>
<br><font size=2 face="sans-serif">____________________________________________<br>
George Fitzgerald, Ph.D. &nbsp; &nbsp; &nbsp; gxf[a]accelrys.com<br>
Accelrys, Inc. &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Tel: &nbsp;+1 858 799 5360<br>
10188 Telesis Court &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
Fax: +1 858 799 5100<br>
Suite 100 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Mobile:
+1 858 692 8722<br>
San Diego, CA 92121</font>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td width=40%><font size=1 face="sans-serif"><b>&quot;b wafaa wafaab2*_*yahoo.fr&quot;
&lt;owner-chemistry[a]ccl.net&gt;</b> </font>
<br><font size=1 face="sans-serif">Sent by: owner-chemistry[a]ccl.net</font>
<p><font size=1 face="sans-serif">10/10/2005 05:51 AM</font>
<table border>
<tr valign=top>
<td bgcolor=white>
<div align=center><font size=1 face="sans-serif">Please respond to<br>
&quot;CCL Subscribers&quot; &lt;chemistry[a]ccl.net&gt;</font></div></table>
<br>
<td width=59%>
<table width=100%>
<tr>
<td>
<div align=right><font size=1 face="sans-serif">To</font></div>
<td valign=top><font size=1 face="sans-serif">&quot;Fitzgerald, George
&quot; &lt;gxf[a]accelrys.com&gt;</font>
<tr>
<td>
<div align=right><font size=1 face="sans-serif">cc</font></div>
<td valign=top>
<tr>
<td>
<div align=right><font size=1 face="sans-serif">Subject</font></div>
<td valign=top><font size=1 face="sans-serif">CCL: Condensed Fukui Functions</font></table>
<br>
<table>
<tr valign=top>
<td>
<td></table>
<br></table>
<br>
<br>
<br><font size=3>Dear CCLers,</font>
<br><font size=3>We have some problems in the prediction of reactivity
when we calculate condensed Fukui functions with the finite difference
approximation using N, N-1 and N+1 systems. </font>
<br><font size=3>In your opinion, what is the best method for the calculation
of these indexes ?</font>
<br><font size=3>Which population analysis do you suggest ?</font>
<br><font size=3>Sincerely</font>
<div align=center>
<p></div>
--=_alternative 00563FD588257097_=--


From owner-chemistry@ccl.net Tue Oct 11 13:22:01 2005
From: "Noel O Boyle no228^-^cam.ac.uk" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Re: Where can you publish articles on software?
Message-Id: <-29543-051011114735-32472-R5yhVjSN3QD3cGxMFS2cAA]|[server.ccl.net>
X-Original-From: "Noel O'Boyle" <no228,;,cam.ac.uk>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain
Date: Tue, 11 Oct 2005 16:47:22 +0100
Mime-Version: 1.0


Sent to CCL by: "Noel O'Boyle" [no228:+:cam.ac.uk]
On Tue, 2005-10-11 at 16:23 +0200, Michel Petitjean
ptitjean-.-itodys.jussieu.fr wrote:
> Sent to CCL by: Michel Petitjean [ptitjean . itodys.jussieu.fr]
> To: chemistry^^ccl.net
> Subject: CCL: Re: Where can you publish articles on software?
> 
> This programme is surely useful, but the editors of research journals
> would probably not accept it for publication. If this kind of article
> is acceptable, I guess that many people would produce tons of technical
> programmes
This is exactly what I think *should* be encouraged! If we look at
bioinformatics, the latest issue of "BMC Bioinformatics" has 7
software articles (this journal has an impact factor of 5.42); the
latest issue of "Bioinformatics" has 9 'Application Notes' (this journal
has an impact factor of 5.74). There is a real interest in useful
software that can make it easier to do science.

>  and have hundreds of papers in their CV, then apply for
> some full Professor position without having done any scientific research.
I don't think this has happened in bioinformatics, but I understand your
point. However, I think that the benefits to the community outweigh this
possibility.

> Publishing programmes for computational chemistry (or other) means
> (a) creating an original algorithm, and (b) programming it, and (c)
> running it on suitable data of interest.
> 
> Regrettably, numerous molecular modeling papers published on the basis
> of step (c) alone bear the same value that papers involving (a)+(b)+(c).
So where is the encouragement for me to write software that can help
other people? To deal with bug reports, feature requests, installation
problems. (You are probably familiar with this also, with your software)

In addition, science should involve building on someone else's work, not
reinventing the wheel. Wouldn't it be better if authors made their code
available so that others could use it? Otherwise every person who wants
to do a particular type of charge analysis, for example, has to read the
algorithm, write the code, and get their result. During my PhD I found
this to be the case for Hirshfeld Population Analysis. I spent a week
and a half reinventing the wheel (and not very well).

This is why I would like to be able to publish an article on a program.

Regards,
Noel


From owner-chemistry@ccl.net Tue Oct 11 13:57:00 2005
From: "Chas Simpson csimpson-,-hydrogen.cem.uct.ac.za" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: W:Test driven development/XP etc. in scientific software development
Message-Id: <-29544-051011115258-2406-Su4vH7lTbEjv7D6a/Z5Evg%%server.ccl.net>
X-Original-From: "Chas  Simpson" <csimpson(!)hydrogen.cem.uct.ac.za>


Sent to CCL by: "Chas  Simpson" [csimpson(0)hydrogen.cem.uct.ac.za]
Hi All,

Ive noted that the regular debates over the merits of Fortran vs C/C++ liken to religious debates with each group furiously defending its position. Personally, the advantage of the relative small performance gain of one language over another is almost nullified by the rate at which hardware is developing. The cost that I find more important is that of maintenance, support and the difficulty of adding enhancements to the software. With this in mind, Im interested in how extensively the following coding techniques/tools (which are extensively employed in business software development) are used in the development of scientific software in both academia and industry.

1. Test driven development (i.e., Unit tests, style guides, continual integration, etc.)
2. Agile development
3. XP (Extreme programming)
4. Software patterns 
5. Other tools such as source control, code coverage, code generators, IDEs other than VI and emacs, etc.

A quick search on the Net revealed that the number and quality of software development tools available for Fortran and C++ were severely lacking in comparison with alternative languages such as Java or C. Perhaps Im wrong. 

Please add to the list if Ive missed anything you feel is important. I will summarize the results.

Thanks,

Chas


From owner-chemistry@ccl.net Tue Oct 11 14:32:00 2005
From: "Jonathan Brecher jsb__cambridgesoft.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: Where can you publish articles on software?
Message-Id: <-29545-051011113813-24003-pim2JxRVHdT+yVuwgui01g^server.ccl.net>
X-Original-From: Jonathan Brecher <jsb|-|cambridgesoft.com>
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Date: Tue, 11 Oct 2005 09:37:43 -0400
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Sent to CCL by: Jonathan Brecher [jsb],[cambridgesoft.com]
At 4:45 AM -0400 10/11/05, Noel O Boyle no228 ~~ cam.ac.uk wrote:
>Where can one publish articles on programs that are of general interest
>to computational chemists, but which do not contain new algorithms?
>
>For example, I have a program that parses the output of the logfiles of
>certain computational chemistry programs, shows the progress of the
>calculation graphically and can convolute some spectra. I would say that
>this is of general interest (judging by the number of downloads), but I
>cannot figure out whether any journals would accept an article
>describing the software (which is freely available, and open source).

JCIM (the former JCICS) is pretty flexible about accepting papers 
that describe new software.  But *please* don't waste everyone's time 
if you're simply looking for publicity.  Find something 
scientifically interesting to say, or don't say anything.

I once reviewed a paper that spent most of a page describing the 
behavior of a program's About Box.  That paper didn't exactly get 
high marks from me...


Jonathan Brecher
jsb^-^cambridgesoft.com


From owner-chemistry@ccl.net Tue Oct 11 15:07:01 2005
From: "Perry E. Metzger perry() piermont.com" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: Re: Where can you publish articles on software?
Message-Id: <-29546-051011145719-13223-x+6Rmy6ORdbaFLdSqYo6OQ-*-server.ccl.net>
X-Original-From: "Perry E. Metzger" <perry:_:piermont.com>
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Date: Tue, 11 Oct 2005 14:57:13 -0400
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Sent to CCL by: "Perry E. Metzger" [perry++piermont.com]

"Noel O'Boyle" writes:
>> 
>> This programme is surely useful, but the editors of research journals
>> would probably not accept it for publication. If this kind of article
>> is acceptable, I guess that many people would produce tons of technical
>> programmes
>
> This is exactly what I think *should* be encouraged!

Yup...

>> Publishing programmes for computational chemistry (or other) means
>> (a) creating an original algorithm, and (b) programming it, and (c)
>> running it on suitable data of interest.
>> 
>> Regrettably, numerous molecular modeling papers published on the basis
>> of step (c) alone bear the same value that papers involving (a)+(b)+(c).

> So where is the encouragement for me to write software that can help
> other people? To deal with bug reports, feature requests, installation
> problems. (You are probably familiar with this also, with your software)
>
> In addition, science should involve building on someone else's work, not
> reinventing the wheel. Wouldn't it be better if authors made their code
> available so that others could use it? Otherwise every person who wants
> to do a particular type of charge analysis, for example, has to read the
> algorithm, write the code, and get their result. During my PhD I found
> this to be the case for Hirshfeld Population Analysis. I spent a week
> and a half reinventing the wheel (and not very well).
>
> This is why I would like to be able to publish an article on a program.

Everything you say here makes sense. Science cannot progress on the
attitude that tool building is an unimportant activity (it is not) or
if we discourage tool building, or if we treat our tools as though
sharing them with others would somehow be negative instead of an
unmitigated positive thing.

One great thing about open source (and I mean real open source, not
the pseudo-open source that frequently is found in the Computational
Chemistry world) is that it can be built on and everyone can share in
the benefits of the improvements, just as we all share in the body of
ideas that is science and try to contribute back so that the knowledge
base increases.

(When I say "pseudo-open", I mean the typical "you can use this for
free but only if you send us a letter in triplicate, and don't dare
alter it or publish the altered code". What is interesting about open
source is *not* the price of the code -- it is the freedom to take
parts of it, or improve it, or rearrange it to fix new problems.)


Perry


From owner-chemistry@ccl.net Tue Oct 11 15:42:01 2005
From: "Alexandre Hocquet alexandre.hocquet.#.eeigm.inpl-nancy.fr" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: W:Condensed Fukui functions
Message-Id: <-29547-051011130332-10322-oatAmKE087cx0nEMscctvw#server.ccl.net>
X-Original-From: "Alexandre  Hocquet" <alexandre.hocquet.:.eeigm.inpl-nancy.fr>


Sent to CCL by: "Alexandre  Hocquet" [alexandre.hocquet;;eeigm.inpl-nancy.fr]
Although Hirshfeld population analyses have been recommended by Parr and others as theoretically sound within the framework of conceptual dft, some papers (well, err, i cannot help quoting mine : Journal of Molecular Structure: THEOCHEM, Volume 686, Issues 1-3, 25 October 2004, Pages 213-218 
Alexandre Hocquet, Alejandro Toro-Labb and Henry Chermette) describe the fact that Hirshfeld charges generate practical problems when they are used to calculate condensed fukui functions.
Hope this helps,
*********************************************** 
Alexandre Hocquet

Recherche :
Laboratoire de Chimie-Physique Macromoleculaire 
UMR CNRS-INPL 7568  BP 451 54001 Nancy cedex
fax : 33.3.83.37.99.77
Alexandre.Hocquet_-_ensic.inpl-nancy.fr
http://www.ensic.inpl-nancy.fr/ENSIC/LCPM/Francais/pagperso/hocquet.htm

Enseignement :
Ecole Europenne d'Ingnieurs en Gnie des Matriaux
6, rue Bastien Lepage 54010 Nancy Cedex
Alexandre.Hocquet_-_eeigm.inpl-nancy.fr
http://www.eeigm.inpl-nancy.fr/

Soutenez le mouvement SAUVONS LA RECHERCHE : http://recherche-en-danger.apinc.org/

***********************************************


From owner-chemistry@ccl.net Tue Oct 11 16:17:00 2005
From: "DELIA SOTO sotodelia ~ hotmail.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: PDB in Amber
Message-Id: <-29548-051011124455-24198-6wLar54wKAFuGwz0cmMrTQ]![server.ccl.net>
X-Original-From: "DELIA SOTO" <sotodelia++hotmail.com>
Content-Type: text/html; charset=iso-8859-1; format=flowed
Date: Tue, 11 Oct 2005 15:57:15 +0000
Mime-Version: 1.0


Sent to CCL by: "DELIA SOTO" [sotodelia]![hotmail.com]
<html><div style='background-color:'><DIV class=RTE>Hi</DIV>
<DIV class=RTE>I`m new in Amber and I have a question</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>What I can do to read, in leap,&nbsp;a PDB file created in Chem3D?</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>&nbsp;</DIV></div></html>


From owner-chemistry@ccl.net Tue Oct 11 17:15:00 2005
From: "Joaquin Barroso Flores joaco_barroso**yahoo.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: NBO deletion analysis error
Message-Id: <-29549-051011153112-8176-vJiL/gGK9oFU/oCQHQ6T6Q!^!server.ccl.net>
X-Original-From: Joaquin Barroso Flores <joaco_barroso:-:yahoo.com>
Content-Transfer-Encoding: 8bit
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Date: Tue, 11 Oct 2005 13:31:03 -0500 (CDT)
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Sent to CCL by: Joaquin Barroso Flores [joaco_barroso]![yahoo.com]
--0-182488929-1129055463=:42466
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Greetings,
 
I am trying to do an NBO deletion analysis on Organotin compounds and I keep runing into the following warning:
 

***** WARNING ***** The variational principle has been

violated and the above deletion energy is invalid!!

Probable cause: A deletion was attempted that did not 

have as high symmetry as was employed in the integral

and SCF computation. REMEDY: Redo computation without

symmetry if this non-symmetry-conserving deletion is still

desired.

 
I've run this calculations with the NoSymm option but the warning persists. I've run them both in G03w and G98. I have previously done similar calculations on related systems with no problem. Any pointers on this one? All help is appreciated. Thanks



**********************************************************
                 Q. Joaquín Barroso Flores

                 Instituto de Química UNAM 
      Correo Alterno: joaquin_barroso#,#correo.unam.mx
**********************************************************
		
---------------------------------
  Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx 
--0-182488929-1129055463=:42466
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

<DIV>
<DIV>Greetings,</DIV>
<DIV>&nbsp;</DIV>
<DIV>I am trying to do an NBO deletion analysis on Organotin compounds and I keep runing into the following warning:</DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=2>
<P>***** WARNING ***** The variational principle has been</P>
<P>violated and the above deletion energy is invalid!!</P>
<P>Probable cause: A deletion was attempted that did not </P>
<P>have as high symmetry as was employed in the integral</P>
<P>and SCF computation. REMEDY: Redo computation without</P>
<P>symmetry if this non-symmetry-conserving deletion is still</P>
<P>desired.</P></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>I've run this calculations with the NoSymm option but the warning persists. I've run them both in G03w and G98. I have previously done similar calculations on related systems with no problem.&nbsp;Any pointers on this one? All help is appreciated. Thanks</DIV></DIV><BR><BR>**********************************************************<br>                 Q. Joaquín Barroso Flores<br><br>                 Instituto de Química UNAM <br>      Correo Alterno: joaquin_barroso#,#correo.unam.mx<br>**********************************************************<p>
		<hr size=1>  
Do You Yahoo!? 
La mejor conexión a Internet y <b>2GB</b> extra a tu correo por $100 al mes. <a href="http://net.yahoo.com.mx">http://net.yahoo.com.mx</a> 

--0-182488929-1129055463=:42466--


From owner-chemistry@ccl.net Tue Oct 11 18:27:01 2005
From: "Andy Holder holdera[#]umkc.edu" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: W:CCL: Where can you publish articles on software?
Message-Id: <-29550-051011153749-12066-RRXW0uduH6eNa0DORipOfg*_*server.ccl.net>
X-Original-From: "Andy  Holder" <holdera+*+umkc.edu>


Sent to CCL by: "Andy  Holder" [holdera%umkc.edu]
In reply to:

> This programme is surely useful, but the editors of research journals
> would probably not accept it for publication. If this kind of article
> is acceptable, I guess that many people would produce tons of technical
> programmes
>>This is exactly what I think *should* be encouraged! If we look at
>>bioinformatics, the latest issue of "BMC Bioinformatics" has 7
>>software articles (this journal has an impact factor of 5.42); the
>>latest issue of "Bioinformatics" has 9 'Application Notes' (this journal
>>has an impact factor of 5.74). There is a real interest in useful
>>software that can make it easier to do science.

I am the editor of the Journal of Molecular Graphics and Modelling, and we specifically EXCLUDE program announcements/descriptions from our pages.  Programs are not original research, but may be implementations of original research.

Being a former member of the Dewar group, they certainly published a large number of papers on semiempirical methods, but never published any article on AMPAC itself.  These programs were even run on just a few examples of "suitable data of interest"!  The algorithm is perhaos worthy of publication, and the program can certainly be mentioned, but is not in and of itself worthy of the valuable space in a research journal.

Comparison to various other journals with high impact factors is anecdotal at best.  The data from JMGM indicate that our IF went DOWN when we included these item and has been steadily increasing since we eliminated them.  But that could also have been for a number of other reasons.

My 0.02.

Regards, Andy Holder

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 
JJJJJJJJ MMM   MMM   GGG   MMM   MMM |        ANDREW J. HOLDER
   JJ     MM   MM   GG GG   MM   MM  |              Editor
   JJ     MMM MMM  GG       MMM MMM  |J. of Molclr Grphcs & Modelling
   JJ     MM M MM  GG GGGG  MM M MM  |        Dept. of Chemistry
JJ JJ    MM  M  MM  GG GG  MM  M  MM |  Univ. of Missouri-Kansas City
  JJ                 GGG             |      Kansas City, MO  64110
                                     |        holdera##umkc.edu
   Published by Elsevier Science     | (816)235-2293 * (816)235-6543F
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From owner-chemistry@ccl.net Tue Oct 11 19:02:00 2005
From: "hao guo guohao78|hotmail.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: a question about AutoDock
Message-Id: <-29551-051011154528-16162-STdvdGzwO2XglisF9/FbVA^^^server.ccl.net>
X-Original-From: "hao guo" <guohao78]|[hotmail.com>
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Date: Tue, 11 Oct 2005 18:58:22 +0000
Mime-Version: 1.0


Sent to CCL by: "hao guo" [guohao78{}hotmail.com]
Hello, everyone.
I am a user of AutoDock software.  I am using this software to model the 
interactions between a protein and a palmitic acid molecule.  I do know this 
palmitic acid molecule forms a chemical  bond with a specific residue of the 
protein. I want to use the autodock to get its confomation after it is 
bonded with the protein.  But during the docking process, I do not know how 
to add constraints to represent this chemical bond.  If you have any idea, 
please tell me.  Any suggestions will be appreciated.  Thanks a lot for your 
help and patience.


From owner-chemistry@ccl.net Tue Oct 11 19:41:01 2005
From: "Peter Gannett pgannett__hsc.wvu.edu" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: PDB in Amber
Message-Id: <-29552-051011193904-24421-CAK1rNZtKnzdLXYfJj0oRQ_._server.ccl.net>
X-Original-From: "Peter Gannett" <pgannett-$-hsc.wvu.edu>
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Date: Tue, 11 Oct 2005 19:39:45 -0400
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Sent to CCL by: "Peter Gannett" [pgannett]_[hsc.wvu.edu]
This is a MIME message. If you are reading this text, you may want to 
consider changing to a mail reader or gateway that understands how to 
properly handle MIME multipart messages.

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First, you probably ought to consider getting on the amber reflector (go
to http://amber.scripps.edu ) and posting your question there.  You are
likely to have other questions and this will probably be the most useful
place to get answers to amber related problems.  
 
As to your file problem...I am not a chem3d user.  My guess is that
chem3d is including connectivity information.  If so, then just strip
out this portion of the file and just try to load the coordinates.  
 
Pete

>>> owner-chemistry_-_ccl.net 10/11/2005 11:57:15 AM >>>

Sent to CCL by: "DELIA SOTO" [sotodelia]![hotmail.com] Hi
I`m new in Amber and I have a question
 
What I can do to read, in leap, a PDB file created in Chem3D?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=__Part7B597951.0__=
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<BODY style=3D"MARGIN: 4px 4px 1px; FONT: 10pt Tahoma">
<DIV>First, you probably ought to consider getting on the amber reflector =
(go to <A href=3D"http://amber.scripps.edu">http://amber.scripps.edu</A> ) =
and posting your question there.&nbsp; You are likely to have other =
questions and this will probably be the most useful&nbsp;place to get =
answers to amber related problems.&nbsp; </DIV>
<DIV>&nbsp;</DIV>
<DIV>As to your file problem...I am not a chem3d user.&nbsp; My guess is =
that chem3d is including connectivity information.&nbsp; If so, then just =
strip out this portion of the file and just try to load the coordinates.&nb=
sp; </DIV>
<DIV>&nbsp;</DIV>
<DIV>Pete<BR><BR>&gt;&gt;&gt; owner-chemistry_-_ccl.net 10/11/2005 11:57:15 =
AM &gt;&gt;&gt;<BR></DIV>
<DIV style=3D"COLOR: #000000">Sent to CCL by: "DELIA SOTO" [sotodelia]![hot=
mail.com]=20
<DIV>
<DIV class=3DRTE>Hi</DIV>
<DIV class=3DRTE>I`m new in Amber and I have a question</DIV>
<DIV class=3DRTE>&nbsp;</DIV>
<DIV class=3DRTE>What I can do to read, in leap,&nbsp;a PDB file created =
in Chem3D?</DIV>
<DIV class=3DRTE>&nbsp;</DIV>
<DIV class=3DRTE>&nbsp;</DIV></DIV>-=3D This is automatically added to =
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From owner-chemistry@ccl.net Tue Oct 11 20:16:00 2005
From: "jle jle^^theworld.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Re: Where can you publish articles on software?
Message-Id: <-29553-051011194650-28792-3F2t6WQnsa8hiL/d6JSt0w[*]server.ccl.net>
X-Original-From: jle <jle++theworld.com>
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Sent to CCL by: jle [jle-.-theworld.com]

On Oct 11, 2005, at 11:47 AM, Noel O Boyle no228^-^cam.ac.uk wrote:
>
> In addition, science should involve building on someone else's work, 
> not
> reinventing the wheel. Wouldn't it be better if authors made their code
> available so that others could use it? Otherwise every person who wants
> to do a particular type of charge analysis, for example, has to read 
> the
> algorithm, write the code, and get their result. During my PhD I found
> this to be the case for Hirshfeld Population Analysis. I spent a week
> and a half reinventing the wheel (and not very well).
>
> This is why I would like to be able to publish an article on a program.
>
Well, if what they want is done by a commercially available program,
they can purchase and use it without concern (assuming most such
programs, particularly in the QM field) are validated and tested well.

Otherwise, they can make the code available under the suitable open-
source license or as a binary distribution on a website and post 
pointers
on places such as CCL.  We're still quite a small community, so if 
something's
good and available, it'll turn up, or be Google-able.

Writing the code's actually the smallest about of work.  Debugging it,
validating it, maintaining it and possibly porting it are usually way 
more
work :-).

Joe Leonard
jle*|*theworld.com