From owner-chemistry@ccl.net Tue Sep  6 05:21:00 2011
From: "Jozsef Csontos jcsontos.lists|*|gmail.com" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: B3LYP for conformer energies (no dispersion)
Message-Id: <-45396-110906051609-18742-vayRbmlatS9mjA8q/njIMQ-*-server.ccl.net>
X-Original-From: Jozsef Csontos <jcsontos.lists##gmail.com>
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Date: Tue, 06 Sep 2011 11:15:56 +0200
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Sent to CCL by: Jozsef Csontos [jcsontos.lists{}gmail.com]

Dear List Members,

Could someone, please, give me some indications/references/benchmark 
data for the performance/reliability of B3LYP in the calculation of 
relative conformer energies?
In my case dispersion hardly takes part in the stabilization of the 
conformers.

Thank you,

Jozsef


From owner-chemistry@ccl.net Tue Sep  6 05:56:00 2011
From: "Daniel Cappel daniel.cappel]|[schrodinger.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: visualize mutiple xyz coordinates
Message-Id: <-45397-110906051429-11860-FZFXbLoEprKep67wtBFVjw^^^server.ccl.net>
X-Original-From: Daniel Cappel <daniel.cappel++schrodinger.com>
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Date: Tue, 6 Sep 2011 11:08:14 +0200
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Sent to CCL by: Daniel Cappel [daniel.cappel]![schrodinger.com]
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Hi Tarzan!

You may try PyMOL for this.

www.pymol.org

Best, Daniel

On Mon, Sep 5, 2011 at 4:40 PM, tarzan h tarzan11_11..yahoo.com <
owner-chemistry.:.ccl.net> wrote:

>
> Sent to CCL by: "tarzan  h" [tarzan11_11^_^yahoo.com]
> hi all
> It would be nice if someone can suggest a  software to visulaise multiple
> molecule coordinates in the xyz format in the single file.
>
> thanx in advance
>
>
>


--=20
Schr=F6dinger Knowledge Base: http://www.schrodinger.com/kb/
Direct Support Phone: +49 (621) 438 55173

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

Dr. Daniel Cappel - Applications Scientist
phone: +49 (621) 438 55172
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Hi Tarzan!<br><br>You may try PyMOL for this.<br><br><a href=3D"http://www.=
pymol.org">www.pymol.org</a><br><br>Best, Daniel<br><br><div class=3D"gmail=
_quote">On Mon, Sep 5, 2011 at 4:40 PM, tarzan h tarzan11_11..<a href=3D"ht=
tp://yahoo.com">yahoo.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner=
-chemistry.:.ccl.net">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: &quot;tarzan =A0h&quot; [tarzan11_11^_^<a href=3D"http://ya=
hoo.com" target=3D"_blank">yahoo.com</a>]<br>
hi all<br>
It would be nice if someone can suggest a =A0software to visulaise multiple=
 molecule coordinates in the xyz format in the single file.<br>
<br>
thanx in advance<br>
<br>

<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Schr=F6dinger Knowledge=
 Base: <a href=3D"http://www.schrodinger.com/kb/" target=3D"_blank">http://=
www.schrodinger.com/kb/</a><br>Direct Support Phone: +49 (621) 438 55173<br=
><br>

----------------------------------------------------------------<br><br>Dr.=
 Daniel Cappel - Applications Scientist<br>phone: +49 (621) 438 55172<br>fa=
x: +49 (621) 438 55555<br>cell: +49 (175) 4334727<br><br>------------------=
----------------------------------------------<br>

Sitz der Gesellschaft/Registered Office:<br>Schr=F6dinger GmbH, Dynamostr. =
13, D-68165 Mannheim<br>Gesch=E4ftsf=FChrer/Managing Director:=A0 Dr. J=F6r=
g Weiser<br>Handelsregister/Commercial Register: HRB 9583 Amtsgericht Mannh=
eim<br>



--e89a8f646aa512969a04ac422c98--


From owner-chemistry@ccl.net Tue Sep  6 06:30:00 2011
From: "Sergio Manzetti sergio.manzetti---gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL:G: Snap shot generator for Gaussian outputs
Message-Id: <-45398-110906055343-6233-evSruPNsywUXhpMfYYkt0w..server.ccl.net>
X-Original-From: Sergio Manzetti <sergio.manzetti#,#gmail.com>
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Date: Tue, 6 Sep 2011 11:53:37 +0200
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Sent to CCL by: Sergio Manzetti [sergio.manzetti-#-gmail.com]
--20cf3079b6203028d804ac42cd44
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Dear CCLs, are there ways of generating "frameshots" as log files or chk
files for gaussian optimization runs?

In other words generating a series of files for a reaction path?

Best wishes

Sergio

--20cf3079b6203028d804ac42cd44
Content-Type: text/html; charset=ISO-8859-1

Dear CCLs, are there ways of generating &quot;frameshots&quot; as log files or chk files for gaussian optimization runs?<br><br>In other words generating a series of files for a reaction path?<br><br>Best wishes<br><br>Sergio<br>

--20cf3079b6203028d804ac42cd44--


From owner-chemistry@ccl.net Tue Sep  6 08:07:00 2011
From: "Pierre Archirel pierre.archirel(!)u-psud.fr" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: conformation analysis with B3LYP
Message-Id: <-45399-110906080523-4217-vZV5m8OWvZ4WXil7RPJhGg+/-server.ccl.net>
X-Original-From: "Pierre  Archirel" <pierre.archirel]![u-psud.fr>
Date: Tue, 6 Sep 2011 08:05:21 -0400


Sent to CCL by: "Pierre  Archirel" [pierre.archirel-*-u-psud.fr]
This is an answer to Jozsef Csontos

I have published an accurate conformation analysis in solution using B3LYP
and the PCM method with UFF radii, for a 44 atom oxazolidinone, see:

M. Branca, V. Alezra, C. Kouklovski, P. Archirel
Tetrahedron (64) 2008 pp. 1743-1752

Pierre Archirel
LCP
University of Orsay, France
pierre.archirel()u-psud.fr


From owner-chemistry@ccl.net Tue Sep  6 08:41:00 2011
From: "Gkourmpis, Thomas Thomas.Gkourmpis]_[borealisgroup.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL:G: Snap shot generator for Gaussian outputs
Message-Id: <-45400-110906070147-25256-5c75bLucz3YvDPJO1fT9qA*_*server.ccl.net>
X-Original-From: "Gkourmpis, Thomas" <Thomas.Gkourmpis]*[borealisgroup.com>
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Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis+/-borealisgroup.com]

--_000_2BD27C21A5B53C4AB53F403FC915A182186F04FAA5CMS02mignetwo_
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Sergio Hi=0D=0A=0D=0AThe easiest way (in my opinion at least) to generate a=
 movie for a reaction along the reaction pathway is via the IRC calculation=
=2E If you perform an IRC all the different steps are plotted together in t=
he GaussView window=2E On the top left hand side you will see the current a=
nd total number of IRC points (1 of 13 for example) and next to it there is=
 a green button=2E That is the play/stop button that can animate the proces=
s=2E If you use the File tab there is an entry called Save Movie=2E You cho=
se this and the movie is saved=2E=0D=0A=0D=0AI hope this helps=2E If you ha=
ve difficulties let me know and I'll be happy to assist=0D=0A=0D=0AThomas=
=0D=0A=0D=0AFrom: owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ec=
om[a]ccl=2Enet [mailto:owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=
=2Ecom[a]ccl=2Enet] On Behalf Of Sergio Manzetti sergio=2Emanzetti---gmail=2E=
com=0D=0ASent: Tuesday, September 06, 2011 11:54 AM=0D=0ATo: Gkourmpis, Tho=
mas=0D=0ASubject: CCL:G: Snap shot generator for Gaussian outputs=0D=0A=0D=
=0ADear CCLs, are there ways of generating "frameshots" as log files or chk=
 files for gaussian optimization runs?=0D=0A=0D=0AIn other words generating=
 a series of files for a reaction path?=0D=0A=0D=0ABest wishes=0D=0A=0D=0AS=
ergio=0D=0A=0D=0A=0D=0AThis Email and any files transmitted with it are con=
fidential and=0D=0Aintended solely for the use of the individual or the ent=
ity to whom=0D=0Ait is addressed=2E If you have received this Email by erro=
r, please=0D=0Anotify the sender and delete the material from any storage d=
evice=2E=0D=0ABorealis extends no warranties and makes no representations a=
s to=0D=0Athe accuracy or completeness of the information provided=2E It is=
 the=0D=0Acustomer's responsibility to inspect and test our products and=0D=
=0Atechnical advice in order to satisfy itself as to the suitability=0D=0Ao=
f the products and technical advice for the customer's particular=0D=0Apurp=
ose=2E
--_000_2BD27C21A5B53C4AB53F403FC915A182186F04FAA5CMS02mignetwo_
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<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:x=3D"urn:schemas-microsoft-com:office:excel" xmlns:html=3D"http://www=
=2Ew3=2Eorg/TR/REC-html40" xmlns:m=3D"http://schemas=2Emicrosoft=2Ecom/offi=
ce/2004/12/omml" xmlns=3D"http://www=2Ew3=2Eorg/TR/REC-html40"><head><meta =
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ut v:ext=3D"edit">=0D=0A<o:idmap v:ext=3D"edit" data=3D"1" />=0D=0A</o:shap=
elayout></xml><![endif]--></head><body lang=3DEN-GB link=3Dblue vlink=3Dpur=
ple><div class=3DWordSection1><p class=3DMsoNormal style=3D'text-align:just=
ify'><span style=3D'font-size:10=2E0pt;font-family:"Arial","sans-serif";col=
or:#1F497D'>Sergio Hi<o:p></o:p></span></p><p class=3DMsoNormal style=3D'te=
xt-align:justify'><span style=3D'font-size:10=2E0pt;font-family:"Arial","sa=
ns-serif";color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=3DMsoNormal s=
tyle=3D'text-align:justify'><span style=3D'font-size:10=2E0pt;font-family:"=
Arial","sans-serif";color:#1F497D'>The easiest way (in my opinion at least)=
 to generate a movie for a reaction along the reaction pathway is via the I=
RC calculation=2E If you perform an IRC all the different steps are plotted=
 together in the GaussView window=2E On the top left hand side you will see=
 the current and total number of IRC points (1 of 13 for example) and next =
to it there is a green button=2E That is the play/stop button that can anim=
ate the process=2E If you use the File tab there is an entry called Save Mo=
vie=2E You chose this and the movie is saved=2E<o:p></o:p></span></p><p cla=
ss=3DMsoNormal style=3D'text-align:justify'><span style=3D'font-size:10=2E0=
pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p></span>=
</p><p class=3DMsoNormal style=3D'text-align:justify'><span style=3D'font-s=
ize:10=2E0pt;font-family:"Arial","sans-serif";color:#1F497D'>I hope this he=
lps=2E If you have difficulties let me know and I&#8217;ll be happy to assi=
st<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-align:justify'><=
span style=3D'font-size:10=2E0pt;font-family:"Arial","sans-serif";color:#1F=
497D'><o:p>&nbsp;</o:p></span></p><p class=3DMsoNormal style=3D'text-align:=
justify'><span style=3D'font-size:10=2E0pt;font-family:"Arial","sans-serif"=
;color:#1F497D'>Thomas<o:p></o:p></span></p><p class=3DMsoNormal><span styl=
e=3D'font-size:10=2E0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:=
p>&nbsp;</o:p></span></p><div style=3D'border:none;border-top:solid #B5C4DF=
 1=2E0pt;padding:3=2E0pt 0cm 0cm 0cm'><p class=3DMsoNormal><b><span lang=3D=
EN-US style=3D'font-size:10=2E0pt;font-family:"Tahoma","sans-serif"'>From:<=
/span></b><span lang=3DEN-US style=3D'font-size:10=2E0pt;font-family:"Tahom=
a","sans-serif"'> owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ec=
om[a]ccl=2Enet [mailto:owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=
=2Ecom[a]ccl=2Enet] <b>On Behalf Of </b>Sergio Manzetti sergio=2Emanzetti---g=
mail=2Ecom<br><b>Sent:</b> Tuesday, September 06, 2011 11:54 AM<br><b>To:</=
b> Gkourmpis, Thomas<br><b>Subject:</b> CCL:G: Snap shot generator for Gaus=
sian outputs<o:p></o:p></span></p></div><p class=3DMsoNormal><o:p>&nbsp;</o=
:p></p><p class=3DMsoNormal>Dear CCLs, are there ways of generating &quot;f=
rameshots&quot; as log files or chk files for gaussian optimization runs?<b=
r><br>In other words generating a series of files for a reaction path?<br><=
br>Best wishes<br><br>Sergio<o:p></o:p></p></div></body></html>=0D=0AThis E=
mail and any files transmitted with it are confidential and intended solely=
 for the use of the individual or the entity to whom it is addressed=2E If =
you have received this Email by error, please notify the sender and delete =
the material from any storage device=2E Borealis extends no warranties and =
makes no representations as to the accuracy or completeness of the informat=
ion provided=2E It is the customer's responsibility to inspect and test our=
 products and technical advice in order to satisfy itself as to the suitabi=
lity of the products and technical advice for the customer's particular pur=
pose=2E
--_000_2BD27C21A5B53C4AB53F403FC915A182186F04FAA5CMS02mignetwo_--


From owner-chemistry@ccl.net Tue Sep  6 09:16:01 2011
From: "Lars Goerigk lars.goerigk[#]uni-muenster.de" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: B3LYP for conformer energies (no dispersion)
Message-Id: <-45401-110906071824-6852-RsUCIPoDAgb6kyAJv6+kWw- -server.ccl.net>
X-Original-From: Lars Goerigk <lars.goerigk%a%uni-muenster.de>
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Date: Tue, 06 Sep 2011 13:18:15 +0200 (CEST)
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Sent to CCL by: Lars Goerigk [lars.goerigk*_*uni-muenster.de]
Dear Joszef,

you could have a look at the GMTKN30 benchmarks in PCCP (2011), 13, 6670 and
at the Supporting Information of that paper. There you can also see the effect
of dispersion and comparisons of 47 functionals with each other for four
conformer test sets. Maybe those data can help you with your problem. However,
B3LYP is not necessarily the best choice for relative energies of conformers.
If you can afford it, you should try double-hybrids, which are close to the
accuracy of CCSD(T)/CBS reference data. Also other hybrids are more accurate
than B3LYP. Moreover, the GMTKN30 results also indicate the importance of
dispersion for conformers, due to intramolecular effects; dispersion effects
do not only influence the energy values themselves but, more importantly, the
energetic orders of the conformers and thus all conclusions drawn from those
results. I suggest to have a look at dispersion effects in your case by using
DFT-D schemes, which does not involve any significant additional computational
effort.

Regards,
Lars

--
Dr. Lars Goerigk
Theoretical Organic Chemistry
Westfälische-Wilhelms Universität Münster
Organisch-Chemisches Institut
Corrensstr. 40
48149 Münster
Germany


Jozsef Csontos jcsontos.lists|*|gmail.com schrieb am 2011-09-06:

> Sent to CCL by: Jozsef Csontos [jcsontos.lists{}gmail.com]

> Dear List Members,

> Could someone, please, give me some indications/references/benchmark
> data for the performance/reliability of B3LYP in the calculation of
> relative conformer energies?
> In my case dispersion hardly takes part in the stabilization of the
> conformers.

> Thank you,

> Jozsef



> -= This is automatically added to each message by the mailing script
> =-
> To recover the email address of the author of the message, please
> change> Conferences:
> http://server.ccl.net/chemistry/announcements/conferences/

From owner-chemistry@ccl.net Tue Sep  6 09:51:00 2011
From: "Angel Fernandez angel_dfer{=}hotmail.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Gaussian 09: Operation out of range (l122.exe)
Message-Id: <-45402-110906043205-538-ubKBCpHyTvdU1vpIxYHHBA*server.ccl.net>
X-Original-From: "Angel  Fernandez" <angel_dfer---hotmail.com>
Date: Tue, 6 Sep 2011 04:32:03 -0400


Sent to CCL by: "Angel  Fernandez" [angel_dfer###hotmail.com]
Hello. I am trying to run DFT calculations on a system with one less electron 
than I have already calculated. With the same input words (only different 
charge and multiplicity), everything works ok for original system but not 
now.

I have checked free space and usual causes of this ending. I appreciate some 
help, since I've tried different bases or options, and I can't get it done.

Input commands:

#P B3LYP/gen pseudo=read Guess=(Fragment=2,only) pop=none Charge

I put some lines of the error output:


 (Enter /util/software/G09RevA02/g09/l122.exe)
 Operation on file out of range.
FileIO: IOper= 2 IFilNo(1)=  -522 Len=        4591 IPos=        4591 
Q=*****************


 dumping /fiocom/, unit = 1 NFiles =    57 SizExt =    524288 WInBlk =      
8192
                   defal = T LstWrd =   364085248 FType=2 FMxFil=10000

 Number           0          0        501        502        503        507        
508        512
 Base     109731840  363560960      90112     417792     262144     270336     
516096     434176
 End      130744320  364085248      91112     428783     265718     275506     
516126     443455
 End1     130744320  364085248      98304     434176     270336     278528     
524288     450560
 Wr Pntr  109666304  172924928      90112     417792     262144     270336     
516096     434176
 Rd Pntr  109666304  172924928      90159     417792     262144     270336     
516096     443455
 Length    21012480     524288       1000      10991       3574       5170         
30       9279

.. (More things like these go in the middle).


dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk =      
8192
                   defal = T LstWrd =       65536 FType=2 FMxFil=10000

 Number           0
 Base         40960
 End          65536
 End1         65536
 Wr Pntr      40960
 Rd Pntr      40960
 Length       24576
 Error termination in NtrErr:
 NtrErr Called from FileIO.


From owner-chemistry@ccl.net Tue Sep  6 10:26:01 2011
From: "Jun Zhang coolrainbow.:.yahoo.cn" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL:G: Snap shot generator for Gaussian outputs
Message-Id: <-45403-110906091153-19220-fcIp3GgMp+OCm9qOfA95ZA===server.ccl.net>
X-Original-From: Jun Zhang <coolrainbow],[yahoo.cn>
Content-Type: multipart/alternative; boundary="0-976514438-1315314700=:60354"
Date: Tue, 6 Sep 2011 21:11:40 +0800 (CST)
MIME-Version: 1.0


Sent to CCL by: Jun Zhang [coolrainbow[a]yahoo.cn]
--0-976514438-1315314700=:60354
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable

Hello Sergio:=0A=C2=A0=0ATo my knowledge, the only way is to hack the sourc=
e code (I know someone had done this, he wrote a code and insert it into GA=
USSIAN to generate chk files =0Afor each point along the reaction path), of=
 course, you should have the source copyright.=0A=C2=A0=0AMaybe IOP could d=
o, but I have not found how=0A=0A------------------------------------------=
----------------------=0AJun Zhang (coolrainbow a yahoo.cn)=0AComputational C=
hemistry Group=0ANo.94, Weijinlu=0ANankai University =0ATianjin, China=0A=
=0A=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A Sergio Manzetti sergio.manzetti---g=
mail.com <owner-chemistry a ccl.net>=0A=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "=
Zhang, Jun " <coolrainbow a yahoo.cn>=0A=E5=8F=91=E9=80=81=E6=97=A5=
=E6=9C=9F=EF=BC=9A 2011=E5=B9=B49=E6=9C=886=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=
=BA=8C, =E4=B8=8B=E5=8D=88 5:53=0A=E4=B8=BB=E9=A2=98: CCL:G: Snap shot gene=
rator for Gaussian outputs=0A=0A=0ADear CCLs, are there ways of generating =
"frameshots" as log files or chk files for gaussian optimization runs?=0A=
=0AIn other words generating a series of files for a reaction path?=0A=0ABe=
st wishes=0A=0ASergio
--0-976514438-1315314700=:60354
Content-Type: text/html; charset=utf-8
Content-Transfer-Encoding: quoted-printable

<html><body><div style=3D"color:#000; background-color:#fff; font-family:ti=
mes new roman, new york, times, serif;font-size:12pt"><div><span>Hello Serg=
io:<var id=3D"yui-ie-cursor"></var></span></div><div><span></span>&nbsp;</d=
iv><div><span>To my knowledge, the only way is to hack the source code (I k=
now someone had done this, he wrote a code and insert it into GAUSSIAN to g=
enerate chk files </span></div><div><span>for each point along the reaction=
 path), of course, you should have the source copyright.</span></div><div><=
span></span>&nbsp;</div><div><span>Maybe IOP could do, but I have not found=
 how</span></div><div></div><div>&nbsp;</div><div>-------------------------=
---------------------------------------<br>Jun Zhang (coolrainbow a yahoo.cn)=
<br>Computational Chemistry Group<br>No.94, Weijinlu<br>Nankai University <=
br>Tianjin, China<br></div><div style=3D"font-family: times new roman, new =
york, times, serif; font-size: 12pt;"><div style=3D"font-family: times new
 roman, new york, times, serif; font-size: 12pt;"><font size=3D"2" face=3D"=
Arial"><div style=3D"margin: 5px 0px; padding: 0px; border: 1px solid rgb(2=
04, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class=3D"hr" c=
ontentEditable=3D"false" readonly=3D"true"></div><b><span style=3D"font-wei=
ght: bold;">=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A</span></b> Sergio Manzetti=
 sergio.manzetti---gmail.com &lt;owner-chemistry a ccl.net&gt;<br><b><span st=
yle=3D"font-weight: bold;">=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A</span></b> =
"Zhang, Jun " &lt;coolrainbow a yahoo.cn&gt;<br><b><span style=3D"fon=
t-weight: bold;">=E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A</span></b> 2=
011=E5=B9=B49=E6=9C=886=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=BA=8C, =E4=B8=8B=E5=
=8D=88 5:53<br><b><span style=3D"font-weight: bold;">=E4=B8=BB=E9=A2=98:</s=
pan></b> CCL:G: Snap shot generator for Gaussian outputs<br></font><br><div=
 id=3D"yiv1635373655">Dear CCLs, are there ways of generating "frameshots" =
as log files or chk files for gaussian optimization runs?<br><br>In other w=
ords generating a series of files for a reaction path?<br><br>Best
 wishes<br><br>Sergio<br>=0A</div><br><br></div></div></div></body></html>
--0-976514438-1315314700=:60354--


From owner-chemistry@ccl.net Tue Sep  6 11:02:00 2011
From: "Sergio Manzetti sergio.manzetti(a)gmail.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: Snap shot generator for Gaussian outputs
Message-Id: <-45404-110906102744-29306-Z+govhv+cFrGMa6Et5GKfg^-^server.ccl.net>
X-Original-From: Sergio Manzetti <sergio.manzetti,,gmail.com>
Content-Type: multipart/alternative; boundary=20cf3079bbf818438004ac46a16f
Date: Tue, 6 Sep 2011 16:27:37 +0200
MIME-Version: 1.0


Sent to CCL by: Sergio Manzetti [sergio.manzetti+*+gmail.com]
--20cf3079bbf818438004ac46a16f
Content-Type: text/plain; charset=windows-1252
Content-Transfer-Encoding: quoted-printable

Thank you Thomas. But do I need to input certain values in the Gaussian
input file, in order to save the trajectory?

best wishes

Sergio

On Tue, Sep 6, 2011 at 1:01 PM, Gkourmpis, Thomas Thomas.Gkourmpis]_[
borealisgroup.com <owner-chemistry .. ccl.net> wrote:

> Sergio Hi****
>
> ** **
>
> The easiest way (in my opinion at least) to generate a movie for a reacti=
on
> along the reaction pathway is via the IRC calculation. If you perform an =
IRC
> all the different steps are plotted together in the GaussView window. On =
the
> top left hand side you will see the current and total number of IRC point=
s
> (1 of 13 for example) and next to it there is a green button. That is the
> play/stop button that can animate the process. If you use the File tab th=
ere
> is an entry called Save Movie. You chose this and the movie is saved.****
>
> ** **
>
> I hope this helps. If you have difficulties let me know and I=92ll be hap=
py
> to assist****
>
> ** **
>
> Thomas****
>
> ** **
>
> *From:* owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com#ccl.net[m=
ailto:
> owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com#ccl.net] *On Beha=
lf Of
> *Sergio Manzetti sergio.manzetti---gmail.com
> *Sent:* Tuesday, September 06, 2011 11:54 AM
> *To:* Gkourmpis, Thomas
> *Subject:* CCL:G: Snap shot generator for Gaussian outputs****
>
> ** **
>
> Dear CCLs, are there ways of generating "frameshots" as log files or chk
> files for gaussian optimization runs?
>
> In other words generating a series of files for a reaction path?
>
> Best wishes
>
> Sergio****
> This Email and any files transmitted with it are confidential and intende=
d
> solely for the use of the individual or the entity to whom it is addresse=
d.
> If you have received this Email by error, please notify the sender and
> delete the material from any storage device. Borealis extends no warranti=
es
> and makes no representations as to the accuracy or completeness of the
> information provided. It is the customer's responsibility to inspect and
> test our products and technical advice in order to satisfy itself as to t=
he
> suitability of the products and technical advice for the customer's
> particular purpose.

--20cf3079bbf818438004ac46a16f
Content-Type: text/html; charset=windows-1252
Content-Transfer-Encoding: quoted-printable

Thank you Thomas. But do I need to input certain values in the Gaussian inp=
ut file, in order to save the trajectory?<br><br>best wishes<br><br>Sergio<=
br><br><div class=3D"gmail_quote">On Tue, Sep 6, 2011 at 1:01 PM, Gkourmpis=
, Thomas Thomas.Gkourmpis]_[<a href=3D"http://borealisgroup.com">borealisgr=
oup.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry .. ccl.net=
">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;"><div link=3D"blue" vlink=3D"purple" lang=3D=
"EN-GB"><div><p class=3D"MsoNormal" style=3D"text-align:justify"><span styl=
e=3D"font-size:10.0pt;color:#1F497D">Sergio Hi<u></u><u></u></span></p>
<p class=3D"MsoNormal" style=3D"text-align:justify"><span style=3D"font-siz=
e:10.0pt;color:#1F497D"><u></u>=A0<u></u></span></p><p class=3D"MsoNormal" =
style=3D"text-align:justify"><span style=3D"font-size:10.0pt;color:#1F497D"=
>The easiest way (in my opinion at least) to generate a movie for a reactio=
n along the reaction pathway is via the IRC calculation. If you perform an =
IRC all the different steps are plotted together in the GaussView window. O=
n the top left hand side you will see the current and total number of IRC p=
oints (1 of 13 for example) and next to it there is a green button. That is=
 the play/stop button that can animate the process. If you use the File tab=
 there is an entry called Save Movie. You chose this and the movie is saved=
.<u></u><u></u></span></p>
<p class=3D"MsoNormal" style=3D"text-align:justify"><span style=3D"font-siz=
e:10.0pt;color:#1F497D"><u></u>=A0<u></u></span></p><p class=3D"MsoNormal" =
style=3D"text-align:justify"><span style=3D"font-size:10.0pt;color:#1F497D"=
>I hope this helps. If you have difficulties let me know and I=92ll be happ=
y to assist<u></u><u></u></span></p>
<p class=3D"MsoNormal" style=3D"text-align:justify"><span style=3D"font-siz=
e:10.0pt;color:#1F497D"><u></u>=A0<u></u></span></p><p class=3D"MsoNormal" =
style=3D"text-align:justify"><span style=3D"font-size:10.0pt;color:#1F497D"=
>Thomas<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.0pt;color:#1F497D"><u></=
u>=A0<u></u></span></p><div style=3D"border:none;border-top:solid #B5C4DF 1=
.0pt;padding:3.0pt 0cm 0cm 0cm"><p class=3D"MsoNormal"><b><span style=3D"fo=
nt-size:10.0pt" lang=3D"EN-US">From:</span></b><span style=3D"font-size:10.=
0pt" lang=3D"EN-US"> owner-chemistry+thomas.gkourmpis=3D=3D<a href=3D"http:=
//borealisgroup.com#ccl.net" target=3D"_blank">borealisgroup.com#ccl.net</a=
> [mailto:<a href=3D"mailto:owner-chemistry%2Bthomas.gkourmpis" target=3D"_=
blank">owner-chemistry+thomas.gkourmpis</a>=3D=3D<a href=3D"http://borealis=
group.com#ccl.net" target=3D"_blank">borealisgroup.com#ccl.net</a>] <b>On B=
ehalf Of </b>Sergio Manzetti <a href=3D"http://sergio.manzetti---gmail.com"=
 target=3D"_blank">sergio.manzetti---gmail.com</a><br>
<b>Sent:</b> Tuesday, September 06, 2011 11:54 AM<br><b>To:</b> Gkourmpis, =
Thomas<br><b>Subject:</b> CCL:G: Snap shot generator for Gaussian outputs<u=
></u><u></u></span></p></div><div><div></div><div class=3D"h5"><p class=3D"=
MsoNormal">
<u></u>=A0<u></u></p><p class=3D"MsoNormal">Dear CCLs, are there ways of ge=
nerating &quot;frameshots&quot; as log files or chk files for gaussian opti=
mization runs?<br><br>In other words generating a series of files for a rea=
ction path?<br>
<br>Best wishes<br><br>Sergio<u></u><u></u></p></div></div></div></div>
This Email and any files transmitted with it are confidential and intended =
solely for the use of the individual or the entity to whom it is addressed.=
 If you have received this Email by error, please notify the sender and del=
ete the material from any storage device. Borealis extends no warranties an=
d makes no representations as to the accuracy or completeness of the inform=
ation provided. It is the customer&#39;s responsibility to inspect and test=
 our products and technical advice in order to satisfy itself as to the sui=
tability of the products and technical advice for the customer&#39;s partic=
ular purpose.</blockquote>
</div><br><br clear=3D"all"><br>

--20cf3079bbf818438004ac46a16f--


From owner-chemistry@ccl.net Tue Sep  6 16:00:00 2011
From: "Pezhman Zarabadi-Poor pzarabadip=gmail.com" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL:G: Emission spectra simulation in G09w
Message-Id: <-45405-110906145243-22244-WmQEvv2jlar82RvkNCpBvg#%#server.ccl.net>
X-Original-From: "Pezhman  Zarabadi-Poor" <pzarabadip||gmail.com>
Date: Tue, 6 Sep 2011 14:52:41 -0400


Sent to CCL by: "Pezhman  Zarabadi-Poor" [pzarabadip\a/gmail.com]
Dear CCL users,

One of my friend and I tried to do the emission spectra simulation based on 
Gaussian published tutorial on their website:
http://www.gaussian.com/g_tech/g_ur/k_scrf.htm

We have used formaldehyde instead of acetaldehyde for saving time :)
Unfortunately, the job has been died and we got the following error which is 
still unresolved for us:
"PCMU: Requested matrix not present on file"

Can anyone help us?

Regards,
Pezhman Zarabadi-Poor


From owner-chemistry@ccl.net Tue Sep  6 16:46:00 2011
From: "Adam Tenderholt atenderholt]|[gmail.com" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL:G: molecular orbital coeficient
Message-Id: <-45406-110906164512-23548-9lH8Vxz7UkPdIV5BTNGMvg###server.ccl.net>
X-Original-From: Adam Tenderholt <atenderholt+/-gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Tue, 6 Sep 2011 13:45:04 -0700
MIME-Version: 1.0


Sent to CCL by: Adam Tenderholt [atenderholt|a|gmail.com]
Hi Mina,

I think some clarification is in order to make sure we're on the same
page. Some of this has already been addressed by others, but I'll
reiterate.

The coefficients you see in the Gaussian output file are the amount
each basis functions (atom/orbital) contributes to a molecular orbital
(MO). Converting these numbers to a "MO coefficient" requires figuring
out how to divide up electron density. The simplest approach is to
simply square these numbers (called C-squared population analysis);
the sum over all basis functions for a given MO should add to 1.
Another approach proposed by Mulliken is to weight the contribution
based on the overlap between basis functions.

With that said, what exactly are you after? The contribution of
specific atoms to a MO such as the HOMO or LUMO? Or put another way,
for example, are you interested in the %C1 character in the molecular
orbitals? Assuming this is the information you want, the QMForge was
designed for this task. The steps for this are: 1) open a gaussian
logfile (or logfile from another supported QM program); 2) create
"fragments" (e.g. C1, C2, others, etc.) you are interested by clicking
the plus icon (double-clicking a fragment name allows you to rename
it); 3) assign the atoms/orbitals to the fragments by
dragging/dropping; 4) choose Method->Mulliken (or C-squared). Note
that all of the atoms/orbitals have to be assigned to fragments, and
you need iop(3/33=1) in your inputfile for Mulliken.

Hope this helps,

Adam



On Fri, Sep 2, 2011 at 7:34 AM, Mina Haghdadi mhaghdadi2|,|yahoo.co.uk
<owner-chemistry^_^ccl.net> wrote:
>
> Sent to CCL by: Mina Haghdadi [mhaghdadi2*yahoo.co.uk]
> Dear Banderia,
> this program gives the data that is in out put file of gaussian, and MO coeficient is different with
> Mulliken fragment analysis I can't find.
> for example for a special molecule I want to find MO coeficients at reactive sites of it.
> unfortunatly  my problem didn't solve.
> I regard my thanks for your time.
> Does anybody can help?
>
> regards
> M.Haghdadi
>
>
>
> --- On Mon, 29/8/11, Nuno A. G. Bandeira nuno.bandeira__ist.utl.pt <owner-chemistry_-_ccl.net> wrote:
>
>> From: Nuno A. G. Bandeira nuno.bandeira__ist.utl.pt <owner-chemistry_-_ccl.net>
>> Subject: CCL:G: molecular orbital coeficient
>> To: "Haghdadi, Mina " <mhaghdadi2_-_yahoo.co.uk>
>> Date: Monday, 29 August, 2011, 1:00
>>
>> Sent to CCL by: "Nuno A. G. Bandeira"
>> [nuno.bandeira/./ist.utl.pt]
>> I think what you're looking for is a Mulliken fragment
>> analysis. You can do this with a special single point file
>> from Gaussian and QMForge.
>>
>> The latter you can download here:
>>
>> http://faculty.washington.edu/adamlt82/QMForge-11Mar27.zip
>>
>> The documentation is here: http://sourceforge.net/apps/mediawiki/cclib/index.php?title=Main_Page
>>
>> Best wishes,
>>
>> -- Nuno A. G. Bandeira, AMRSC
>> Departamento de Química Física i Inorgánica
>> Despatx 207, N4 - Universitat Rovira i Virgili
>> Campus Sescelades, Carrer Marcel.lí Domingo
>> 43007 Tarragona - SPAIN
>> --
>>
>>
>>
>> -= This is automatically added to each message by the
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