From owner-chemistry@ccl.net Wed Jul 31 03:51:00 2013
From: "Bijan Mondal mondal.bijan[-]gmail.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL: Fenske-Hall Mo study.
Message-Id: <-49043-130731034902-26360-0DuxoG6Ps6N+0SEu3wbymg()server.ccl.net>
X-Original-From: Bijan Mondal <mondal.bijan|,|gmail.com>
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Date: Wed, 31 Jul 2013 13:18:51 +0530
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Sent to CCL by: Bijan Mondal [mondal.bijan(!)gmail.com]
--089e0115ecf0e241c504e2c9f40d
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Dear All,

I want to perform Fenske-Hall MO calculations. Any suggestions for free
program package?
I heard about Jimp2. Could you please suggest me how to set the
calculations and analyze the result?

Many thanks in advance.

With regards,
Bijan

-- 
*"There are no such electron-deficient compounds,*
*             **only theory-deficient chemists." --* R.E. Rundle

Bijan Mondal
Research Scholar
Mob: 7667156593
Department of Chemistry
I.I.T Madras
Chennai

--089e0115ecf0e241c504e2c9f40d
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Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div><div><div><div>Dear All, <br><br></div>I want to perf=
orm Fenske-Hall MO calculations. Any suggestions for free program package?<=
br></div>I heard about Jimp2. Could you please suggest me how to set the ca=
lculations and analyze the result?<br>
<br></div>Many thanks in advance.<br><br></div>With regards,<br>Bijan<br cl=
ear=3D"all"><div><div><div><div><div><div><br>-- <br><div><font style=3D"fo=
nt-family:comic sans ms,sans-serif" color=3D"#33ccff" face=3D"trebuchet ms,=
sans-serif"><span style=3D"color:rgb(0,0,153)"><i><font style=3D"background=
-color:rgb(255,255,255)">&quot;<font><font>There are no</font> such electro=
n-deficient compounds,</font></font></i></span></font></div>
<div><font style=3D"font-family:comic sans ms,sans-serif" color=3D"#33ccff"=
 face=3D"trebuchet ms,sans-serif"><span style=3D"color:rgb(0,0,153)"><i><fo=
nt style=3D"background-color:rgb(255,255,255)"><font>=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0 <b>=A0</b></font></font></i></span></font><font style=3D"font-=
family:comic sans ms,sans-serif"><span style=3D"color:rgb(0,0,153)"><font f=
ace=3D"trebuchet ms,sans-serif"><font><font><font><font style=3D"background=
-color:rgb(255,255,255)"><font color=3D"#000099"><i>only theory-deficient c=
hemists.&quot; --</i> R.E. Rundle<br>
</font></font></font></font></font></font></span></font></div><font style=
=3D"font-family:comic sans ms,sans-serif"><font face=3D"trebuchet ms,sans-s=
erif"><font><font><font><font style=3D"background-color:rgb(255,255,255)"><=
font color=3D"#000099"></font></font></font></font></font></font></font><di=
v>
<font style=3D"font-family:comic sans ms,sans-serif"><span style=3D"color:r=
gb(0,0,153)"></span></font>=A0</div><div><font style=3D"font-family:comic s=
ans ms,sans-serif"><span style=3D"color:rgb(0,0,153)">Bijan Mondal<br>Resea=
rch Scholar</span></font></div>

<div><font style=3D"font-family:comic sans ms,sans-serif"><span style=3D"co=
lor:rgb(0,0,153)">Mob: 7667156593<br>Department of Chemistry<br>I.I.T Madra=
s<br>Chennai</span></font><br></div>
</div></div></div></div></div></div></div>

--089e0115ecf0e241c504e2c9f40d--


From owner-chemistry@ccl.net Wed Jul 31 11:01:00 2013
From: "Jimmy Stewart MrMOPAC]^[att.net" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: New MOPAC runs faster
Message-Id: <-49044-130731105210-28833-nwXavcn0Io9hV0hHZmHa2w,+,server.ccl.net>
X-Original-From: Jimmy Stewart <MrMOPAC**att.net>
Content-Type: multipart/alternative;
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Date: Wed, 31 Jul 2013 08:52:08 -0600
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Sent to CCL by: Jimmy Stewart [MrMOPAC/./att.net]
This is a multi-part message in MIME format.
--------------050603070204090606000702
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               Announcement of Increase in Speed of MOPAC2012

Although MOPAC has been under continuous development over the past thirty
plus years, there have been only small increases in speed in the main,
i.e. non-MOZYME, methods. Various attempts have been made over this period
to make MOPAC run faster. The latest attempt, by a research group headed by
Prof. Dr. Gerd B. Rocha at the Federal University of Paraiba, Brazil, has
been successful. Two modifications have been made: many of the old, slower,
operations have been replaced by the Intel Math Kernel Library, and 
sections
of the code have been parallelized to take advantage of multi-threading.

Details of the modifications can be found at: 
HTTP://WWW.QUANTUM-CHEM.PRO.BR/

These changes have resulted in an increase in speed, as shown in the 
following
table:


Times, in seconds, for a single-point calculation run on a 2 x 2.93 GHz
6-Core Intel Xeon with 16Gb of 1333 DDR3 memory chips Mac Pro computer,
using 12 of the 24 threads

________________________________________________________________________
Species            #atoms        Current     MOPAC2012   MOPAC with MKL and
                              MOPAC2012    with MKL multi-threading
________________________________________________________________________

Naphthalene      18            0.02         0.15            0.02
(H2O)573       1719        3,082.23       584.78           79.30
1G6X           1455        8,612.57     1,240.48          142.07
1RNB (Barnase) 2066       34,372.13     4,108.87          411.26
________________________________________________________________________

In MOPAC, proteins can be modeled using the MOZYME technique, however, that
technique is limited to closed shell RHF calculations. This means that 
proteins
with free radical sites, excited state proteins, and proteins containing 
iron,
chromium or other transition metal atoms should not be modeled using 
MOZYME.

The new MOPAC reduces the computation time so that conventional MOPAC 
methods
can now be used for many proteins. This means that it is now practical 
to use
conventional MOPAC methods - RHF-CI and UHF - for modeling most of the 
smaller
proteins, and by implication that it will be possible to model many 
systems that
currently cannot or should not be modeled using MOZYME.

The improved MOPAC is available in the usual forms: Windows, Linux, and 
Mac, and
can be downloaded from  http://openmopac.net/

Details of the modifications to the MOPAC2012 code, as well as some 
results,
benchmarks and an application in biomolecules, can be found in the 
following publication:

Maia, J. D. C.; Urquiza Carvalho, G. A.; Mangueira, C. P.; Santana, S. 
R.; Cabral, L. A. F.;
Rocha, G. B., Journal of Chemical Theory and Computation 2012, 8, 
3072:3081.
DOI: 10.1021/ct3004645

We would appreciate any suggestions or bug reports that could further 
improve the
parallel version of MOPAC, so please don't hesitate to contact us.

Best wishes,

Jimmy





-- 
  James J. P. Stewart
  Stewart Computational Chemistry
  15210 Paddington Circle
  Colorado Springs CO 80921-2512
  USA

Tel: USA+(719) 488-9416


--------------050603070204090606000702
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Content-Transfer-Encoding: 7bit

<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    <font face="Courier New, Courier, monospace"><br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Announcement of Increase in Speed of MOPAC2012<br>
      <br>
      Although MOPAC has been under continuous development over the past
      thirty <br>
      plus years, there have been only small increases in speed in the
      main, <br>
      i.e. non-MOZYME, methods. Various attempts have been made over
      this period <br>
      to make MOPAC run faster. The latest attempt, by a research group
      headed by <br>
      Prof. Dr. Gerd B. Rocha at the Federal University of Paraiba,
      Brazil, has <br>
      been successful. Two modifications have been made: many of the
      old, slower, <br>
      operations have been replaced by the Intel Math Kernel Library,
      and sections <br>
      of the code have been parallelized to take advantage of
      multi-threading. <br>
      <br>
      Details of the modifications can be found at:
      <a class="moz-txt-link-freetext" href="HTTP://WWW.QUANTUM-CHEM.PRO.BR/">HTTP://WWW.QUANTUM-CHEM.PRO.BR/</a><br>
      <br>
      These changes have resulted in an increase in speed, as shown in
      the following <br>
      table:<br>
      <br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
      Times, in seconds, for a single-point calculation run on a 2 x
      2.93 GHz <br>
      6-Core Intel Xeon with 16Gb of 1333 DDR3 memory chips Mac Pro
      computer, <br>
      using 12 of the 24 threads<br>
      <br>
________________________________________________________________________<br>
      Species&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #atoms&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Current&nbsp;&nbsp;&nbsp;&nbsp; MOPAC2012&nbsp;&nbsp; MOPAC
      with MKL and<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; MOPAC2012&nbsp;&nbsp;&nbsp; with MKL&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      multi-threading<br>
________________________________________________________________________<br>
      <br>
      Naphthalene&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 18&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.02&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.15&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.02<br>
      (H2O)573&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1719&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3,082.23&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 584.78&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 79.30<br>
      1G6X&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1455&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8,612.57&nbsp;&nbsp;&nbsp;&nbsp; 1,240.48&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 142.07<br>
      1RNB (Barnase) 2066&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 34,372.13&nbsp;&nbsp;&nbsp;&nbsp; 4,108.87&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 411.26<br>
________________________________________________________________________<br>
      <br>
      In MOPAC, proteins can be modeled using the MOZYME technique,
      however, that <br>
      technique is limited to closed shell RHF calculations. This means
      that proteins <br>
      with free radical sites, excited state proteins, and proteins
      containing iron, <br>
      chromium or other transition metal atoms should not be modeled
      using MOZYME. <br>
      <br>
      The new MOPAC reduces the computation time so that conventional
      MOPAC methods <br>
      can now be used for many proteins. This means that it is now
      practical to use <br>
      conventional MOPAC methods - RHF-CI and UHF - for modeling most of
      the smaller<br>
      proteins, and by implication that it will be possible to model
      many systems that <br>
      currently cannot or should not be modeled using MOZYME.<br>
      <br>
      The improved MOPAC is available in the usual forms: Windows,
      Linux, and Mac, and <br>
      can be downloaded from&nbsp; <a class="moz-txt-link-freetext" href="http://openmopac.net/">http://openmopac.net/</a><br>
      <br>
      Details of the modifications to the MOPAC2012 code, as well as
      some results, <br>
      benchmarks and an application in biomolecules, can be found in the
      following publication:<br>
      <br>
      Maia, J. D. C.; Urquiza Carvalho, G. A.; Mangueira, C. P.;
      Santana, S. R.; Cabral, L. A. F.; <br>
      Rocha, G. B., Journal of Chemical Theory and Computation 2012, 8,
      3072:3081. <br>
      DOI: 10.1021/ct3004645<br>
      <br>
      We would appreciate any suggestions or bug reports that could
      further improve the <br>
      parallel version of MOPAC, so please don&#8217;t hesitate to contact us.<br>
      <br>
      Best wishes,<br>
      <br>
      Jimmy<br>
      <br>
      <br>
      <br>
      <br>
      <br>
    </font>
    <pre class="moz-signature" cols="72"><font face="Courier New, Courier, monospace">-- 
 James J. P. Stewart
 Stewart Computational Chemistry
 15210 Paddington Circle
 Colorado Springs CO 80921-2512
 USA

Tel: USA+(719) 488-9416 </font></pre>
  </body>
</html>

--------------050603070204090606000702--


From owner-chemistry@ccl.net Wed Jul 31 17:38:00 2013
From: "Radoslaw Kaminski rkaminski.rk[*]gmail.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL:G: External electric field
Message-Id: <-49045-130730233910-729-YdLAKeclsz81pc6UEe4i3A : server.ccl.net>
X-Original-From: Radoslaw Kaminski <rkaminski.rk---gmail.com>
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Date: Tue, 30 Jul 2013 23:38:21 -0400
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Sent to CCL by: Radoslaw Kaminski [rkaminski.rk**gmail.com]
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Dear Thomas,

Rather an off-topic, but it is very interesting to investigate this issue
experimentally. Niels Hansen published a set of many intersting articles
for that. An example is given below:

R. Guillot, P. Fertey, N.K. Hansen, P. Alle, E. Elkaim, C. Lecomte,
Diffraction study of the piezoelectric properties of low quartz, Eur. Phys.
J. B 42, 373=96380 (2004)

The literature given there might be of some interest to you. There are also
some earlier works by Graafsma and Coppens, who did similar experiments for
molecular crystals (which might a bit more relevant to what you are
interested in).

Best wishes,

Radek


On 30 July 2013 04:39, Thomas Exner texner/agmx.net <owner-chemistry]=[ccl.ne=
t
> wrote:

>
> Sent to CCL by: Thomas Exner [texner^gmx.net]
> Dear CCLers:
>
> I am interested in the influences of an external electric field on the
> electron density distribution and structure of my molecule. It is very ea=
sy
> to include such a field in the quantum calculations using e.g. gaussian b=
ut
> I am wondering how I can relate such microscopic fields to the macroscopi=
c
> field. The used atomic units sound extremely large.
>
> Thank you very much for your advice.
> Thomas
>
>
>
> -=3D This is automatically added to each message by the mailing script =
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--=20
Radoslaw Kaminski, Ph.D. Eng.
Postdoctoral Research Associate
Department of Chemistry, University at Buffalo
The State University of New York
747 Natural Sciences Complex
Buffalo, NY 14260-3000, USA
http://www.chem.uw.edu.pl/people/RKaminski/

--001a11c278a46d105804e2c677fa
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Dear Thomas,<br><br>Rather an off-topic, but it is very interesting to inve=
stigate this issue experimentally. Niels Hansen published a set of many int=
ersting articles for that. An example is given below:<br><br>R. Guillot, P.=
 Fertey, N.K. Hansen, P. Alle, E. Elkaim, C. Lecomte, Diffraction study of =
the piezoelectric properties of low quartz, Eur. Phys. J. B 42, 373=96380 (=
2004)<br>

<br>The literature given there might be of some interest to you. There are =
also some earlier works by Graafsma and Coppens, who did similar experiment=
s for molecular crystals (which might a bit more relevant to what you are i=
nterested in).<br>

<br>Best wishes,<br><br>Radek<br><br><br><div class=3D"gmail_quote">On 30 J=
uly 2013 04:39, Thomas Exner texner/<a href=3D"http://agmx.net">agmx.net</a=
> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry]=[ccl.net" target=
=3D"_blank">owner-chemistry]=[ccl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><br>
Sent to CCL by: Thomas Exner [texner^<a href=3D"http://gmx.net" target=3D"_=
blank">gmx.net</a>]<br>
Dear CCLers:<br>
<br>
I am interested in the influences of an external electric field on the elec=
tron density distribution and structure of my molecule. It is very easy to =
include such a field in the quantum calculations using e.g. gaussian but I =
am wondering how I can relate such microscopic fields to the macroscopic fi=
eld. The used atomic units sound extremely large.<br>


<br>
Thank you very much for your advice.<br>
Thomas<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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<br>
<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br><div dir=3D"ltr">Radosl=
aw Kaminski, Ph.D. Eng.<br>Postdoctoral Research Associate<br>Department of=
 Chemistry, University at Buffalo<br>The State University of New York<br>74=
7 Natural Sciences Complex   <br>

Buffalo, NY 14260-3000, USA<br><a href=3D"http://www.chem.uw.edu.pl/people/=
RKaminski/" target=3D"_blank">http://www.chem.uw.edu.pl/people/RKaminski/</=
a></div>

--001a11c278a46d105804e2c677fa--