From owner-chemistry@ccl.net Mon Jun 30 03:14:01 2014
From: "Chris Swain swain#,#mac.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: Fortran on a Mac
Message-Id: <-50295-140630031241-5234-V66vVtIFFugP70yKsCAxwQ[A]server.ccl.net>
X-Original-From: Chris Swain <swain(0)mac.com>
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=windows-1252
Date: Mon, 30 Jun 2014 08:12:33 +0100
MIME-version: 1.0


Sent to CCL by: Chris Swain [swain:mac.com]
Hi,

I maintain a website intended to act as a resource for Chemists using Apple Macintosh computers (www.macinchem.org) . I was recently asked if I could compile a resource page for using Fortran on a Mac, this I did and somewhat surprisingly it has turned out to be one of the months most popular pages with readers spending 3-4 minutes reading the page.

The page can be found here, http://www.macinchem.org/reviews/fortran/fortran.php.

I’m not a big Fortran user so if anyone has suggestions for additions I’d be delighted to hear about them.

Cheers

Chris


From owner-chemistry@ccl.net Mon Jun 30 06:24:00 2014
From: "Michel Petitjean petitjean.chiral() gmail.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: Fortran on a Mac
Message-Id: <-50296-140630062149-16514-b5hqq+2z4FWi7Y7+WB89QQ : server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral]*[gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Mon, 30 Jun 2014 12:21:43 +0200
MIME-Version: 1.0


Sent to CCL by: Michel Petitjean [petitjean.chiral]![gmail.com]
I am a fortran developper producing chemistry and bioinformatics
freewares for linux and mac, so I am verry happy to learn that your
website encountered success.
May I suggest to add some information about the following compilation flags:
-static-libgcc : includes all necessary system routines in the binary
and thus avoids error messages at runtime when some library is missing
on the user computer
-mmacosx-version-min=10.1 : generates binaries able to work under
several os x versions
-fno-underscoring : supresses the trailing undersore for names of
functions and subroutines (but then you must take care about
conflicting names)
These flags are highly useful for developpers although not always well known.
Thank you.
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral,+,gmail.com (preferred),
        michel.petitjean,+,univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

2014-06-30 9:12 GMT+02:00 Chris Swain swain#,#mac.com <owner-chemistry,+,ccl.net>:
>
> Sent to CCL by: Chris Swain [swain:mac.com]
> Hi,
>
> I maintain a website intended to act as a resource for Chemists using Apple Macintosh computers (www.macinchem.org) . I was recently asked if I could compile a resource page for using Fortran on a Mac, this I did and somewhat surprisingly it has turned out to be one of the months most popular pages with readers spending 3-4 minutes reading the page.
>
> The page can be found here, http://www.macinchem.org/reviews/fortran/fortran.php.
>
> I’m not a big Fortran user so if anyone has suggestions for additions I’d be delighted to hear about them.
>
> Cheers
>
> Chris
>


From owner-chemistry@ccl.net Mon Jun 30 08:21:00 2014
From: "Shawkat Islam sislam-*-swin.edu.au" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL:G: Reading Basic centre error in Gaussian Output file
Message-Id: <-50297-140629195425-17215-PBr6OyQ3Gu1C2h2YNXcCKA-$-server.ccl.net>
X-Original-From: Shawkat Islam <sislam]*[swin.edu.au>
Content-Language: en-US
Content-Type: multipart/alternative;
	boundary="_000_4C31A2EEF4AF6C4E82D86FCE91D7A2BCF2309Cgspex03dsswinedua_"
Date: Sun, 29 Jun 2014 23:54:15 +0000
MIME-Version: 1.0


Sent to CCL by: Shawkat Islam [sislam[]swin.edu.au]
--_000_4C31A2EEF4AF6C4E82D86FCE91D7A2BCF2309Cgspex03dsswinedua_
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

Hi,
I want to use 2 different basic sets for my calculation. One is an interbal=
 Gaussian basic set but another one I have to give manually in input. I wro=
te Gen in the command line but I found End of file reading basis center in =
output file
Here is the input file:
%chk=3DFreq.chk
# HF/Gen pop=3Dfull

After the XYZ coordinate, I wrote 6-31G(d) for C,H which is an internal Gau=
ssian basic set

C H 0
6-31G(d)
****
Here I wrote the inpurt for a modified basic set which is not an Gaussian b=
asic set
***
I saw in previous discussions that I have remove Gen from route line. So ho=
w can I input for the other basic set.

Thanks in advance

Regards,
Shawkat Islam


--_000_4C31A2EEF4AF6C4E82D86FCE91D7A2BCF2309Cgspex03dsswinedua_
Content-Type: text/html; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D"urn:schemas-micr=
osoft-com:office:office" xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" xmlns=3D"http:=
//www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Dus-ascii"=
>
<meta name=3D"Generator" content=3D"Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
:+:font-face
	{font-family:Helvetica;
	panose-1:2 11 6 4 2 2 2 2 2 4;}
:+:font-face
	{font-family:Helvetica;
	panose-1:2 11 6 4 2 2 2 2 2 4;}
:+:font-face
	{font-family:Calibri;
	panose-1:2 15 5 2 2 2 4 3 2 4;}
:+:font-face
	{font-family:"Comic Sans MS";
	panose-1:3 15 7 2 3 3 2 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0cm;
	margin-bottom:.0001pt;
	font-size:11.0pt;
	font-family:"Calibri","sans-serif";
	mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
	{mso-style-priority:99;
	color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{mso-style-priority:99;
	color:purple;
	text-decoration:underline;}
span.EmailStyle17
	{mso-style-type:personal-compose;
	font-family:"Calibri","sans-serif";
	color:windowtext;}
.MsoChpDefault
	{mso-style-type:export-only;
	font-family:"Calibri","sans-serif";
	mso-fareast-language:EN-US;}
:+:page WordSection1
	{size:612.0pt 792.0pt;
	margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
	{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext=3D"edit">
<o:idmap v:ext=3D"edit" data=3D"1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=3D"EN-AU" link=3D"blue" vlink=3D"purple">
<div class=3D"WordSection1">
<p class=3D"MsoNormal">Hi,<o:p></o:p></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">I want=
 to use 2 different basic sets for my calculation. One is an interbal Gauss=
ian basic set but another one I have to give manually in
 input. I wrote Gen in the command line but I found <b>End of file reading =
basis center in output file
<o:p></o:p></b></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">Here i=
s the input file:
<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">%chk=
=3DFreq.chk<o:p></o:p></span></p>
<p class=3D"MsoNormal"><b><span style=3D"font-size:10.5pt;font-family:&quot=
;Helvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white"># H=
F/Gen pop=3Dfull<o:p></o:p></span></b></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white"><o:p>&=
nbsp;</o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">After =
the XYZ coordinate, I wrote 6-31G(d) for C,H which is an internal Gaussian =
basic set<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white"><o:p>&=
nbsp;</o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">C H 0<=
o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">6-31G(=
d)<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">****</=
span><o:p></o:p></p>
<p class=3D"MsoNormal"><b><span style=3D"font-size:10.5pt;font-family:&quot=
;Helvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">Her=
e I wrote the inpurt for a modified basic set which is not an Gaussian basi=
c set<o:p></o:p></span></b></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.5pt;font-family:&quot;He=
lvetica&quot;,&quot;sans-serif&quot;;color:#444444;background:white">***</s=
pan><o:p></o:p></p>
<p class=3D"MsoNormal"><b>I saw in previous discussions that I have remove =
Gen from route line. So how can I input for the other basic set.<o:p></o:p>=
</b></p>
<p class=3D"MsoNormal"><b><o:p>&nbsp;</o:p></b></p>
<p class=3D"MsoNormal"><b>Thanks in advance<o:p></o:p></b></p>
<p class=3D"MsoNormal"><span style=3D"mso-fareast-language:EN-AU"><o:p>&nbs=
p;</o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Comic Sans MS&quot;=
;mso-fareast-language:EN-AU">Regards,<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Comic Sans MS&quot;=
;mso-fareast-language:EN-AU">Shawkat Islam</span><span style=3D"mso-fareast=
-language:EN-AU"><o:p></o:p></span></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
</body>
</html>

--_000_4C31A2EEF4AF6C4E82D86FCE91D7A2BCF2309Cgspex03dsswinedua_--


From owner-chemistry@ccl.net Mon Jun 30 08:56:00 2014
From: "Rana, Anup rana^chemie.uni-siegen.de" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: Problem with the transition state location with NWChem 6.3
Message-Id: <-50298-140630075449-18314-MB0U5uzchlHv7+v+DF+llQ#%#server.ccl.net>
X-Original-From: "Rana, Anup" <rana:_:chemie.uni-siegen.de>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="iso-8859-1"
Date: Mon, 30 Jun 2014 11:54:39 +0000
MIME-Version: 1.0


Sent to CCL by: "Rana, Anup" [rana*|*chemie.uni-siegen.de]
Hi all,

Myself Anup Rana. I am a PhD student at the Universität Siegen. I am trying to optimize the following transition state in NWChem:

# b3lyp
# nothing.

start TStoP1

echo

memory total 3000 stack 1000 heap 750 global 1250 mb

Title "transition state TS26bis3singlettop1_B3LYP"

charge 0

geometry
C       -2.699293000     -1.625013000     -0.347475000
N       -1.685425000     -2.542235000     -0.625446000
C       -0.749514000     -0.370891000     -0.091519000
C        0.170211000      0.544177000      0.003866000
C       -0.511919000     -1.966830000     -0.378736000
N        0.658547000     -2.536752000     -0.173448000
C        1.848363000     -1.881164000     -0.293579000
C        2.932207000     -2.264492000      0.588376000
C        4.147018000     -1.581945000      0.481250000
C        4.349233000     -0.549347000     -0.474360000
C        3.320309000     -0.194960000     -1.353192000
C        2.071266000     -0.844709000     -1.262703000
C        2.724699000     -3.372019000      1.601677000
H        4.969338000     -1.854762000      1.151628000
H        5.321945000     -0.051096000     -0.532649000
H        3.480785000      0.574615000     -2.114367000
H        1.310008000     -0.669949000     -2.025492000
H        2.392524000     -4.302226000      1.109385000
H        1.933172000     -3.110969000      2.326235000
H        3.654471000     -3.576025000      2.157716000
C       -4.087930000     -1.863031000     -0.385418000
C       -4.963767000     -0.812531000     -0.053065000
C       -4.501431000      0.479961000      0.307800000
C       -3.104677000      0.713922000      0.345014000
C       -2.224245000     -0.323032000      0.011356000
H       -4.465480000     -2.857121000     -0.639796000
H       -6.043414000     -0.999123000     -0.071904000
H       -2.723879000      1.703054000      0.621324000
C       -5.486086000      1.602438000      0.604941000
H       -5.015784000      2.405222000      1.197772000
H       -5.871926000      2.063263000     -0.324678000
H       -6.360566000      1.233674000      1.169122000
C        0.751676000      1.826474000      0.062700000
C        0.742863000      2.697410000     -1.076690000
C        1.359453000      2.294483000      1.272741000
C        1.301469000      3.977603000     -0.993902000
H        0.285134000      2.349143000     -2.006478000
C        1.898807000      3.585101000      1.342854000
H        1.387280000      1.630690000      2.140573000
C        1.877322000      4.430789000      0.213698000
H        1.282163000      4.633096000     -1.870027000
H        2.347689000      3.932547000      2.278307000
H        2.308478000      5.434514000      0.271791000
end

basis
  H library 6-31++G**
  N library 6-31++G**
  C library 6-31++G**
end

dft
  xc b3lyp
  maxiter 1000
  convergence energy 1e-8
  convergence ncydp 100
  convergence ncyds 100
  convergence ncysh 100
  semidirect filesize 0
  grid xfine
end

driver
  maxiter 1000
  tight
  trust 0.3
  SADSTP 0.3
end

task dft saddle
task dft freq

But it is a never ending story; the optimization never completed. I tried several times but it did not converge. Last time I tried up to 470 optimization cycles and again as usual it did not converge. Can anyone, please, suggest me something to overcome the problem?

Similar kind of problem happens with the following transition state:

# blyp
# nothing.

start ts

echo

memory total 3000 stack 1000 heap 750 global 1250 mb

Title "transition state TS26bis3singlettop2_BLYP-D3"

charge 0

geometry
C        2.536692000      3.058367000     -0.103521000
N        1.841928000      2.367510000     -1.097804000
C        3.442816000      0.934998000     -0.048295000
C        4.133606000     -0.165845000      0.095349000
C        2.235772000      1.106355000     -1.048667000
N        1.639062000      0.035540000     -1.558433000
C        2.299290000     -1.149410000     -1.613525000
C        3.687938000     -1.269201000     -2.023339000
C        4.311637000     -2.546322000     -1.924778000
C        3.636087000     -3.647363000     -1.423793000
C        2.265459000     -3.532141000     -1.048200000
C        1.602405000     -2.321123000     -1.159012000
C        4.392911000     -0.218246000     -2.859738000
H        5.351887000     -2.640220000     -2.242321000
H        4.144194000     -4.609243000     -1.339057000
H        1.733278000     -4.402327000     -0.663264000
H        0.556060000     -2.217967000     -0.861854000
H        4.470302000     -0.580706000     -3.897843000
H        3.866629000      0.741792000     -2.871312000
H        5.417100000     -0.056210000     -2.489460000
C        2.379598000      4.405087000      0.260944000
C        3.177161000      4.916776000      1.301216000
C        4.133932000      4.129767000      1.984672000
C        4.285737000      2.772935000      1.618965000
C        3.498540000      2.257592000      0.587089000
H        1.633254000      5.024961000     -0.236321000
H        3.053195000      5.960819000      1.597963000
H        5.013061000      2.142623000      2.135528000
C        5.008830000      4.738852000      3.063087000
H        5.339209000      3.976195000      3.784527000
H        4.470520000      5.524925000      3.614310000
H        5.913524000      5.201162000      2.631203000
C        5.240784000     -0.903622000      0.563704000
C        5.043781000     -2.061570000      1.370737000
C        6.566291000     -0.542072000      0.180104000
C        6.143251000     -2.811092000      1.802440000
H        4.027524000     -2.347067000      1.640193000
C        7.653783000     -1.310469000      0.606662000
H        6.714205000      0.344909000     -0.436030000
C        7.447611000     -2.443655000      1.419532000
H        5.985852000     -3.689589000      2.429778000
H        8.665805000     -1.024007000      0.316670000
H        8.300702000     -3.036210000      1.752832000
C       -1.961175000      1.591211000     -1.043804000
N       -1.253095000      0.394159000     -0.953122000
C       -3.398002000     -0.015827000     -0.235732000
C       -4.392259000     -0.845267000      0.274619000
C       -2.083338000     -0.588102000     -0.461838000
N       -1.715170000     -1.838706000     -0.226413000
C       -2.687502000     -2.660688000      0.281347000
C       -2.331896000     -4.027593000      0.551682000
C       -3.296351000     -4.894865000      1.055147000
C       -4.629152000     -4.466748000      1.301293000
C       -4.996171000     -3.153830000      1.049841000
C       -4.044904000     -2.213528000      0.548465000
C       -0.922061000     -4.498421000      0.275622000
H       -3.019132000     -5.932136000      1.257174000
H       -5.364180000     -5.176756000      1.683841000
H       -6.019560000     -2.824162000      1.227104000
H       -0.673342000     -4.379467000     -0.790713000
H       -0.190470000     -3.895509000      0.835848000
H       -0.805051000     -5.556436000      0.553738000
C       -1.509575000      2.849702000     -1.470271000
C       -2.429260000      3.907799000     -1.442734000
C       -3.768569000      3.742277000     -1.000585000
C       -4.199869000      2.474103000     -0.579067000
C       -3.303949000      1.385757000     -0.602741000
H       -0.474797000      2.990288000     -1.782050000
H       -2.102687000      4.898774000     -1.768144000
H       -5.223310000      2.336237000     -0.232191000
C       -4.715959000      4.927949000     -0.987316000
H       -5.704913000      4.637937000     -0.602225000
H       -4.853764000      5.342307000     -2.000246000
H       -4.329365000      5.743023000     -0.352796000
C       -5.766777000     -0.321693000      0.514190000
C       -6.569504000      0.080600000     -0.573424000
C       -6.277766000     -0.203474000      1.823419000
C       -7.857290000      0.595915000     -0.356651000
H       -6.171831000     -0.005266000     -1.585489000
C       -7.563175000      0.319166000      2.041776000
H       -5.657789000     -0.513579000      2.665758000
C       -8.356776000      0.719764000      0.952317000
H       -8.468269000      0.902414000     -1.207537000
H       -7.943459000      0.414142000      3.060398000
H       -9.356099000      1.124210000      1.121713000
H       -0.263160000      0.253783000     -1.202448000
end

basis
  H library 6-31++G**
  N library 6-31++G**
  C library 6-31G*
end

dft
  xc becke88 lyp
  maxiter 1000
  convergence energy 1e-8
  convergence ncydp 100
  convergence ncyds 100
  convergence ncysh 100
  grid fine
  semidirect filesize 0
  disp vdw 3
end

driver
  maxiter 1000
  tight
end

task dft saddle
task dft freq

I can understand that in this case locating the transition state is bit tricky due to presence of non covalent interaction. If you have any suggestion, please suggest me.

Thank you very much for your time.
 
With regards,
Anup Rana
Universität Siegen
Department Chemie-Biologie
Organische chemie I
Adolf-Reichwein-Str. 2
57068 Siegen, Germany

Email: rana~~chemie.uni-siegen.de


From owner-chemistry@ccl.net Mon Jun 30 14:11:01 2014
From: "Chris Swain swain_-_mac.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Fortran on a Mac
Message-Id: <-50299-140630110754-25954-pIsjdgg6jmppsZvL45Adcw^^server.ccl.net>
X-Original-From: Chris Swain <swain,+,mac.com>
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=windows-1252
Date: Mon, 30 Jun 2014 16:07:34 +0100
MIME-version: 1.0


Sent to CCL by: Chris Swain [swain*o*mac.com]
Dear Michel,

These are exactly the sort of tips that are really useful.

Many Thanks

Chris


Dr Chris Swain BA MA (Cantab) PhD CChem FRSC
Macinchem
Insanely Great Science
swain[-]mac.com
http://www.macinchem.org



On 30 Jun 2014, at 11:21, Michel Petitjean petitjean.chiral() gmail.com <owner-chemistry[-]ccl.net> wrote:

> 
> Sent to CCL by: Michel Petitjean [petitjean.chiral]![gmail.com]
> I am a fortran developper producing chemistry and bioinformatics
> freewares for linux and mac, so I am verry happy to learn that your
> website encountered success.
> May I suggest to add some information about the following compilation flags:
> -static-libgcc : includes all necessary system routines in the binary
> and thus avoids error messages at runtime when some library is missing
> on the user computer
> -mmacosx-version-min=10.1 : generates binaries able to work under
> several os x versions
> -fno-underscoring : supresses the trailing undersore for names of
> functions and subroutines (but then you must take care about
> conflicting names)
> These flags are highly useful for developpers although not always well known.
> Thank you.
> Michel.
> 
> Michel Petitjean
> MTi, INSERM UMR-S 973, University Paris 7,
> 35 rue Helene Brion, 75205 Paris Cedex 13, France.
> Phone: +331 5727 8434; Fax: +331 5727 8372
> E-mail: petitjean.chiral_._gmail.com (preferred),
>        michel.petitjean_._univ-paris-diderot.fr
> http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
> 
> 2014-06-30 9:12 GMT+02:00 Chris Swain swain#,#mac.com <owner-chemistry_._ccl.net>:
>> 
>> Sent to CCL by: Chris Swain [swain:mac.com]
>> Hi,
>> 
>> I maintain a website intended to act as a resource for Chemists using Apple Macintosh computers (www.macinchem.org) . I was recently asked if I could compile a resource page for using Fortran on a Mac, this I did and somewhat surprisingly it has turned out to be one of the months most popular pages with readers spending 3-4 minutes reading the page.
>> 
>> The page can be found here, http://www.macinchem.org/reviews/fortran/fortran.php.
>> 
>> I’m not a big Fortran user so if anyone has suggestions for additions I’d be delighted to hear about them.
>> 
>> Cheers
>> 
>> Chris> 
>


From owner-chemistry@ccl.net Mon Jun 30 14:46:00 2014
From: "zborowsk zborowsk++chemia.uj.edu.pl" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: asymmetrical bending and asymmetric torsional mode for IR spectra
Message-Id: <-50300-140630141739-13168-0umWMV8o7aUCxFfDLEuBbQ a server.ccl.net>
X-Original-From: zborowsk <zborowsk*chemia.uj.edu.pl>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8;
 format=flowed
Date: Mon, 30 Jun 2014 20:17:27 +0200
MIME-Version: 1.0


Sent to CCL by: zborowsk [zborowsk===chemia.uj.edu.pl]
W dniu 2014-06-29 21:30, Abrash, Samuel sabrash%a%richmond.edu 
napisał(a):
> By a combination of the vibrational symmetry, and visualizing the
> modes using a gui interface like jmol, gaussview, avogadro, WebMO,
> etc.
>
>
> Friends, How can I distinguish asymmetrical bending and asymmetric
> torsional mode for IR spectra when numerical data are obtained in
> Quantum chemical calculation?
>  Partha
>
>  --
>  Dr. Partha Sarathi Sengupta
>  Associate Professor
>  Vivekananda Mahavidyalaya, Burdwan

Visualization of vibrational modes is usually not enough.
In order to find position of any vibrational mode in the spectrum you 
should perform Potential Energy Distribution analysis. If possible, 
because there are difficulties with some types of structures. If you 
want to know more you can contact me directly.

regards.

-- 
Krzysztof K. Zborowski
Faculty of Chemistry
Jagiellonian University
3 Ingardena Street
30-060 Krakow
Poland
phone: +48(12)663-2067
email: zborowsk::chemia.uj.edu.pl
gg 3817259
skype kzys70
www.chemia.uj.edu.pl/~zborowsk


From owner-chemistry@ccl.net Mon Jun 30 18:34:00 2014
From: "Adam Tenderholt atenderholt-#-gmail.com" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL:G: Constant Distance between two molecules during optimization in g09
Message-Id: <-50301-140630183024-6130-JS9b6Y1Q5T3Q76NulgrzjQ[a]server.ccl.net>
X-Original-From: Adam Tenderholt <atenderholt(!)gmail.com>
Content-Type: multipart/alternative; boundary=047d7b3a8a5c26968c04fd15349c
Date: Mon, 30 Jun 2014 15:29:57 -0700
MIME-Version: 1.0


Sent to CCL by: Adam Tenderholt [atenderholt]~[gmail.com]
--047d7b3a8a5c26968c04fd15349c
Content-Type: text/plain; charset=UTF-8

Hi Haya,

You can use the ModRedundant option to the Opt keyword. See
http://www.gaussian.com/g_tech/g_ur/k_opt.htm for more details.

Adam



On Sat, Jun 28, 2014 at 10:02 PM, Haya Kornweitz hayak]=[ariel.ac.il <
owner-chemistry[A]ccl.net> wrote:

>
> Sent to CCL by: "Haya  Kornweitz" [hayak.[A].ariel.ac.il]
> Dear CCLs
> I want to perform a DFT optimization calculation for two molecules together
> using g09.
> Is there a way to keep the distance between these two molecules constant
> during
> the optimization?
> Gratefully
> Haya>
>
>

--047d7b3a8a5c26968c04fd15349c
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">Hi Haya,<div><br></div><div>You can use the ModRedundant o=
ption to the Opt keyword. See=C2=A0<a href=3D"http://www.gaussian.com/g_tec=
h/g_ur/k_opt.htm">http://www.gaussian.com/g_tech/g_ur/k_opt.htm</a> for mor=
e details.</div>

<div><br></div><div>Adam</div><div><br></div></div><div class=3D"gmail_extr=
a"><br><br><div class=3D"gmail_quote">On Sat, Jun 28, 2014 at 10:02 PM, Hay=
a Kornweitz hayak]=3D[<a href=3D"http://ariel.ac.il">ariel.ac.il</a> <span =
dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry[A]ccl.net" target=3D"_blank=
">owner-chemistry[A]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: &quot;Haya =C2=A0Kornweitz&quot; [hayak.[A].<a href=3D"http:/=
/ariel.ac.il" target=3D"_blank">ariel.ac.il</a>]<br>
Dear CCLs<br>
I want to perform a DFT optimization calculation for two molecules together=
<br>
using g09.<br>
Is there a way to keep the distance between these two molecules constant du=
ring<br>
the optimization?<br>
Gratefully<br>
Haya<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY[A]ccl.net">CHEMISTRY[A]ccl.n=
et</a> or use:<br>
=C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>=
<br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST[A]ccl.net">CHEM=
ISTRY-REQUEST[A]ccl.net</a> or use<br>
=C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>=
<br>
<br>
Subscribe/Unsubscribe:<br>
=C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtm=
l" target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
=C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/spammers.txt" target=3D"=
_blank">http://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br></div>

--047d7b3a8a5c26968c04fd15349c--