From owner-chemistry@ccl.net Mon Jun 18 00:09:00 2012 From: "MarkG gates.mark]~[gmail.com" To: CCL Subject: CCL: bond length Message-Id: <-47089-120617120849-6304-ix6KYsfe/XlYGoO336yo6A-#-server.ccl.net> X-Original-From: MarkG Content-Type: text/plain; charset=UTF-8 Date: Sun, 17 Jun 2012 12:08:36 -0400 MIME-Version: 1.0 Sent to CCL by: MarkG [gates.mark(-)gmail.com] Newbie question .. I am fixing the bond length between two atoms in my molecule. I would like to actually get the optimization/single point for a series of bond lengths between these atoms incrementing > from the value 1.7A. Is there a way to do this in a single input file instead of individual input files.. ? appreciated. M From owner-chemistry@ccl.net Mon Jun 18 00:44:00 2012 From: "Taras Petrenko taras/./xthch.uni-bonn.de" To: CCL Subject: CCL: Resonance Raman Message-Id: <-47090-120617191622-11667-Y56+/AWJmGoqsypHUpzYFQ*server.ccl.net> X-Original-From: "Taras Petrenko" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=windows-1252; format="flowed" Date: Mon, 18 Jun 2012 01:16:14 +0200 MIME-Version: 1.0 Sent to CCL by: "Taras Petrenko" [taras#xthch.uni-bonn.de] In principle, both resonance and preresonance Raman should be calculated with the same methods. The corresponding intensities can be evaluated in the framework of sum-over-state formulation, or equivalently, in the time domain. In both cases cases Raman intensities depend on the topology of the excited state potential energy and transition moment surfaces. In general, preresonance spectra are dominated by fundamental bands, and higher-order Raman transitions can gain significant intensities for excitations above 0-0 vibronic band. For relative intensities in preresonance Raman several approximate approaches (Savin's formula, gradient method, etc) have been developed, which are, however, not sufficiently accurate in the resonance regime. For more details see the following references: D. J. Tannor and E. J. Heller, Journal of Chemical Physics 77 (1), 202 (1982). E. J. Heller, R. L. Sundberg, and D. Tannor, Journal of Physical Chemistry 86 (10), 1822 (1982). A. B. Myers, R. A. Mathies, D. J. Tannor, and E. J. Heller, Journal of Chemical Physics 77 (8), 3857 (1982). A. B. Myers and R. A. Mathies, in Biological Applications of Raman Spectroscopy, edited by T. G. Spiro (Wiley, New York, 1987), Vol. 2, pp. 1. T. Petrenko and F. Neese, Journal of Chemical Physics 127 (16) (2007). T. Petrenko, K. Ray, K. E. Wieghardt, and F. Neese, Journal of the American Chemical Society 128 (13), 4422 (2006). Taras Petrenko On Sat, 16 Jun 2012 12:27:25 +0530 "Kristin Gleason gleasonkristin__gmail.com" wrote: > Hi , > Can anybody tell how pre-resonance Raman and resonance Raman is >different >> from computational point of view? Also for fluorescence molecule can > pre-resonance Raman will give satisfacory result? > Thanks. From owner-chemistry@ccl.net Mon Jun 18 01:19:00 2012 From: "Taras Petrenko taras.petrenko#,#mpi-mail.mpg.de" To: CCL Subject: CCL: Resonance Raman Message-Id: <-47091-120617202943-6555-dUCGwPz5JgwMk+ZhzLiDsQ-x-server.ccl.net> X-Original-From: Taras Petrenko Content-Type: multipart/alternative; boundary="------------020307050705050006000505" Date: Mon, 18 Jun 2012 02:29:31 +0200 MIME-Version: 1.0 Sent to CCL by: Taras Petrenko [taras.petrenko^^mpi-mail.mpg.de] This is a multi-part message in MIME format. --------------020307050705050006000505 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit In principle, both resonance and preresonance Raman should be calculated with the same methods. The corresponding intensities can be evaluated in the framework of sum-over-state formulation, or equivalently, in the time domain. In both cases cases Raman intensities depend on the topology of the excited state potential energy and transition moment surfaces. In general, preresonance spectra are dominated by fundamental bands, and higher-order Raman transitions can gain significant intensities for excitations above 0-0 vibronic band. For relative intensities in preresonance Raman several approximate approaches (Savin's formula, gradient method, etc) have been developed, which are, however, not sufficiently accurate in the resonance regime. For more details see the following references: D. J. Tannor and E. J. Heller, Journal of Chemical Physics 77 (1), 202 (1982). E. J. Heller, R. L. Sundberg, and D. Tannor, Journal of Physical Chemistry 86 (10), 1822 (1982). A. B. Myers, R. A. Mathies, D. J. Tannor, and E. J. Heller, Journal of Chemical Physics 77 (8), 3857 (1982). A. B. Myers and R. A. Mathies, in Biological Applications of Raman Spectroscopy, edited by T. G. Spiro (Wiley, New York, 1987), Vol. 2, pp. 1. T. Petrenko and F. Neese, Journal of Chemical Physics 127 (16) (2007). T. Petrenko, K. Ray, K. E. Wieghardt, and F. Neese, Journal of the American Chemical Society 128 (13), 4422 (2006). Taras Petrenko --------------020307050705050006000505 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit In principle, both resonance and preresonance Raman should be calculated with the same methods. The corresponding intensities can be evaluated in the framework of sum-over-state formulation, or equivalently, in the time domain. In both cases cases Raman intensities depend on the topology of the  excited state potential energy and transition moment surfaces. In general, preresonance spectra are dominated by fundamental bands, and higher-order Raman transitions can  gain  significant intensities for excitations above 0-0 vibronic band. For relative intensities in preresonance Raman several approximate approaches (Savin's formula, gradient method, etc) have been developed, which are, however, not sufficiently accurate in the resonance regime.

For more details see the following references:
   D. J. Tannor and E. J. Heller, Journal of Chemical Physics 77 (1), 202 (1982).
   E. J. Heller, R. L. Sundberg, and D. Tannor, Journal of Physical Chemistry 86 (10), 1822 (1982).
   A. B. Myers, R. A. Mathies, D. J. Tannor, and E. J. Heller, Journal of Chemical Physics 77 (8), 3857 (1982).
   A. B. Myers and R. A. Mathies, in Biological Applications of Raman Spectroscopy, edited by T. G. Spiro (Wiley, New York, 1987), Vol. 2, pp. 1.
   T. Petrenko and F. Neese, Journal of Chemical Physics 127 (16) (2007).
   T. Petrenko, K. Ray, K. E. Wieghardt, and F. Neese, Journal of the American Chemical Society 128 (13), 4422 (2006).

Taras Petrenko --------------020307050705050006000505-- From owner-chemistry@ccl.net Mon Jun 18 05:05:01 2012 From: "Vera Cathrine vera.cathrine(0)yahoo.com" To: CCL Subject: CCL:G: G09: eq and non-eq solvation for excited state Message-Id: <-47092-120618041914-24078-ylS4OCx1pC8Po79X9csxag[-]server.ccl.net> X-Original-From: "Vera Cathrine" Date: Mon, 18 Jun 2012 04:19:13 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine-*-yahoo.com] Dear All, I am going to calculate the lamba values ( solvent reorganization energy) using TDDFT calculations inside G09. I am familiar with SCRF eq and Non-eq solvation for the excited states (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm). As far as I understand the "non-equilibrium vertical absorption energy" is obtained in step 3 of the example given in SCRF page (by SS solvation of the vertical excitation). But I am actually confused by the term "equilibrium vertical absorption energy". Is this "equilibrium vertical absorption energy" calculated in step 4? Can anyone explain me or refer me to the related steps in the example given in SCRF page? or possibly some example input files? Thank you very much in advance for any help. Best wishes, Vera From owner-chemistry@ccl.net Mon Jun 18 05:39:01 2012 From: "Mehboob Alam mehboob.cu^^gmail.com" To: CCL Subject: CCL:G: bond length Message-Id: <-47093-120618035832-21813-gKt+0WZk73VhCp15rPCSNw!A!server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=e0cb4efe2f4cc284d304c2ba87a7 Date: Mon, 18 Jun 2012 09:58:24 +0200 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu{=}gmail.com] --e0cb4efe2f4cc284d304c2ba87a7 Content-Type: text/plain; charset=ISO-8859-1 Hi Mark, I don't know which software you are using. I know in both ORCA and GAUSSIAN you can do a bond length scan which is a single input calculation and you can find a sample input in the respective manual or you can google it for a sample input. I use DALTON and write a Linux script for doing this. Hope it will help. Best of luck, Mehboob On Sun, Jun 17, 2012 at 6:08 PM, MarkG gates.mark]~[gmail.com < owner-chemistry+/-ccl.net> wrote: > > Sent to CCL by: MarkG [gates.mark(-)gmail.com] > Newbie question .. I am fixing the bond length between two atoms in > my molecule. I would like to actually get the optimization/single > point for a series of bond lengths between these atoms incrementing > > from the value 1.7A. Is there a way to do this in a single input file > instead of individual input files.. ? > > appreciated. > M> > > --e0cb4efe2f4cc284d304c2ba87a7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Mark,

I don't know which software you are using. = I know in both ORCA and GAUSSIAN you can do a bond length scan which is a s= ingle input calculation and you can find a sample input in the respective m= anual or you can google it for a sample input. I use DALTON and write a Lin= ux script for doing this.

Hope it will help.

Best of luc= k,
Mehboob

On Sun, = Jun 17, 2012 at 6:08 PM, MarkG gates.mark]~[gm= ail.com <owner-chemistry+/-ccl.net> wrote:

Sent to CCL by: MarkG [gates.mark(-)gmail.com]
Newbie question .. =A0I am fixing the bond length between two atoms in
my molecule. I would like to actually get the optimization/single
point for a series of bond lengths between these atoms incrementing
> from the value 1.7A. Is there a way to do this in a single input file<= br> instead of individual input files.. ?

appreciated.
M



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--e0cb4efe2f4cc284d304c2ba87a7-- From owner-chemistry@ccl.net Mon Jun 18 06:15:00 2012 From: "Horkel, Ernst ehorkel::ioc.tuwien.ac.at" To: CCL Subject: CCL:G: AW: G: keto-enol-problems Message-Id: <-47094-120618044834-15817-lbfEz6gawauIZ6g78jPxAA~!~server.ccl.net> X-Original-From: "Horkel, Ernst" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 18 Jun 2012 10:48:25 +0200 MIME-Version: 1.0 Sent to CCL by: "Horkel, Ernst" [ehorkel-*-ioc.tuwien.ac.at] Dear Mr. Yeung, Of course you are right, in solution there should be other (additional) effects, I am aware of this; however the problem arose within the calculations of the gas phase structures. In fact, I don't understand how this can happen, as optimizing along both sides of the imaginary frequency should give two energetically lower lying geometries. Or not? BTW, I tried to perform an IRC run, but that failed. I'm working on this. Clarification would be very helpful. Thanks Ernst __________________________________________________ Univ.Ass. Dipl.-Ing. Dr.techn. Ernst Horkel Institute of Applied Synthetic Chemistry, Vienna University of Technology          Tel.: +43-1-58801-163609 Getreidemarkt 9/163OC,                         +43-664-60588-7122 A-1060 Vienna, Austria                   Fax:  +43-1-58801-15499 email: ehorkel:_:ioc.tuwien.ac.at -----Ursprüngliche Nachricht----- Von: owner-chemistry+ehorkel==ioc.tuwien.ac.at:_:ccl.net [mailto:owner-chemistry+ehorkel==ioc.tuwien.ac.at:_:ccl.net] Im Auftrag von Andrew Yeung andrew.yeung]^[chem.tamu.edu Gesendet: Dienstag, 5. Juni 2012 16:16 An: Horkel, Ernst Betreff: CCL:G: keto-enol-problems Sent to CCL by: Andrew Yeung [andrew.yeung,,chem.tamu.edu] Just a thought. In the gas phase, the oscillating hydrogen species is probably the TS of the isomerization. In solution state, trace acid or base should catalyze the tautomerization? Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-06-05 5:11 AM, Ernst Horkel ehorkel(!)ioc.tuwien.ac.at wrote: > Sent to CCL by: "Ernst Horkel" [ehorkel : ioc.tuwien.ac.at] Dear all, > > I have a (at least to me) strange problem when I try to describe a keto-enol tautomerism. The substance under inverstigation is a beta-keto carboxylic acid amide derivative; there is one possible keto-tautomer (having the ketone and the amide a C=O bond). Between the two possible enol-tautomers (one having the O-H on carbon C3 and the other having the O-H on the amide C1), there should be a transition state; I thik I found it, being planar in geometry with the hydrogen oszillating between the two oxygen atoms. A frequency run returned one single imaginary frequency with v=-1086cm-1. So this seems to make sence to me, right? But now the problem: in order to get the both tautomers connected via this TS, I followed the imag.freq. in both directions (manual displacement in gauss view, both in positive and negative direction) and optimized those structures. Results are chemically correct tautomers, frequency runs showed no imaginary frequency. BUT: in one of the tautomers, the ! gi! > bbs free energy is HIGHER than in the TS! How is this possible? Does that make sence (I don't think so). Please help me and leave comments on this, as I'm really stucking at this point for a while. > > some background: > > *planned investigation: realative stability of two tautomers; calculation of the activation energy of the tautomerization. > *used software: Gaussian 09, GaussView 5.0 on a Linux system *level of > theory: DFT, M06-2X, 6-311G(d,p)++, solvent H2O, PCM theory *input > (representative): "opt=tight freq 6-311++g(d,p) scrf=(solvent=water) geom=connectivity int=ultrafine m062x" > *for calculation of "delta G" I used the calculated values in the ".log" file printed in the line (e.g.): "Sum of electronic and thermal Free Energies= -670.274904" > > So please can anyone help (guide) me out of this. Any helpful ideas or comments are really welcome. > > Thank You all in advance, > > best reagrds > > Ernsthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jun 18 09:24:01 2012 From: "Andrew Yeung andrew.yeung- -chem.tamu.edu" To: CCL Subject: CCL:G: bond length Message-Id: <-47095-120618022607-14796-2Eoq11JL2Tz8fvtKMoZ9kg.@.server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 18 Jun 2012 01:26:05 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung!A!chem.tamu.edu] I assume you're using Gaussian? You can use the opt(modredundant) keyword. After the geometry, you input the modredundant section. Take a look at the section entitled "Performing a Relaxed Potential Energy Surface Scan" in http://www.gaussian.com/g_tech/g_ur/k_opt.htm. Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-06-17 11:08 AM, MarkG gates.mark]~[gmail.com wrote: > Sent to CCL by: MarkG [gates.mark(-)gmail.com] > Newbie question .. I am fixing the bond length between two atoms in > my molecule. I would like to actually get the optimization/single > point for a series of bond lengths between these atoms incrementing >> from the value 1.7A. Is there a way to do this in a single input file > instead of individual input files.. ? > > appreciated. > M> > From owner-chemistry@ccl.net Mon Jun 18 10:56:00 2012 From: "Soumen Ghosh soumenrkmrc08 * gmail.com" To: CCL Subject: CCL:G: Gaussian calculation procedure. Message-Id: <-47096-120618075436-20412-DtAmMLLO0lDDc3/R3Evatg*server.ccl.net> X-Original-From: "Soumen Ghosh" Date: Mon, 18 Jun 2012 07:54:35 -0400 Sent to CCL by: "Soumen Ghosh" [soumenrkmrc08,+,gmail.com] How to calculate delocalization energy using gaussian09? Soumen Ghosh soumenrkmrc08**gmail.com IIT Bombay,Powai Mumbai-400076 From owner-chemistry@ccl.net Mon Jun 18 11:30:01 2012 From: "Rajarshi Guha rajarshi.guha * gmail.com" To: CCL Subject: CCL: CINF Lightning Talks - CINFLash (ACS National Meeting, Philadelphia, August 2012) Message-Id: <-47097-120618100156-12214-+WSWHe8948LaxGxHYwkEqg[#]server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=e89a8f3ba8ef5bff4004c2bf9b6f Date: Mon, 18 Jun 2012 10:01:47 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha[A]gmail.com] --e89a8f3ba8ef5bff4004c2bf9b6f Content-Type: text/plain; charset=ISO-8859-1 With the Fall ACS coming up, we are running CINFlash once again - a session of 8 minute lightning talks on any aspect of chemical information and cheminformatics. It's going to run from 4:10pm - 5:30pm on Sunday, August 19. As before, we aren't using PACS - so if you'd like to participate send a very brief abstract (< 100 words) with title to cinf.flash _ gmail.com between June 15 and Aug 10. Visit http://acscinf.org/meetings/244/flash244.php for more details. If you have any questions feel free to mail me at rajarshi.guha _ gmail.com -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science Chair, Division of Chemical Information American Chemical Society --e89a8f3ba8ef5bff4004c2bf9b6f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable With the Fall ACS coming up, we are running=A0CINFlash=A0once again - a session=A0of 8= minute lightning talks on any aspect of chemical information and=A0= cheminformatics.

It's going to run from 4:10pm - 5:30pm on =A0Sund= ay, August 19.=A0As before, we aren't using PACS - s= o if you'd like to participate send a very brief abstract (< 100 wor= ds) with title to cinf.flash _ gmail.= com between June 15 and Aug 10.=A0Visit=A0http://acscinf.org/me= etings/244/flash244.php=A0for more details.

If you have any questions feel free to mail me at=A0<= /span>ra= jarshi.guha _ gmail.com

--
Rajarshi G= uha | http://blog.rguha= .net
NIH Center for Advancing Translational Science

Chair, Division of Chemical Information
American Chemical So= ciety
--e89a8f3ba8ef5bff4004c2bf9b6f-- From owner-chemistry@ccl.net Mon Jun 18 12:41:01 2012 From: "Cory Pye cpye()ap.smu.ca" To: CCL Subject: CCL:G: Gaussian ECP Message-Id: <-47098-120616203823-26058-3nskBZiF2OBv/GFZo8175Q]_[server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sat, 16 Jun 2012 21:48:17 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye-x-ap.smu.ca] Hello, You are mixing two different syntaxes for the cobalt center, both the "standard"nomenclature "SDD" and an explicit function. You should either: 1) extract the full basis set from the EMSL site, and manually add the F function to it, or 2) Add a new line for Co as in Co 0 SDD **** Co 0 <------------ F 1 1.00 0.1019000000D+01 0.1000000000D+01 **** Co 0 SDD It is possible that the arrowed cobalt might need to be replaced with the atom number. -Cory On Sat, 16 Jun 2012, Stephen P George spgeorge-#-ucsd.edu wrote: > > Sent to CCL by: "Stephen P George" [spgeorge a ucsd.edu] > Dear CCL members, > > I am trying to run a calculation on G03 with a Co metal center. I am using the SDD ECP but I wanted to add an f-polarization function to the ECP. However the syntax is giving me some trouble. I was hoping a member might make suggestions as to how to implement this. The inputs I have tried are shown below: > > %chk=PBE0SDD > %NProcShared=8 > # gen pbe1pbe pseudo=read > > Molecule Name > > Atom Description > > C 0 > 6-31G** > **** > H 0 > 6-31G** > **** > N 0 > 6-31G** > **** > Si 0 > 6-31G** > **** > Co 0 > SDD > F 1 1.00 > 0.1019000000D+01 0.1000000000D+01 > **** > > Co 0 > SDD > > > > > and > > > %chk=PBE0SDD > %NProcShared=8 > # gen pbe1pbe pseudo=read > > Molecule Name > > Atom Description > > C 0 > 6-31G** > **** > H 0 > 6-31G** > **** > N 0 > 6-31G** > **** > Si 0 > 6-31G** > **** > Co 0 > SDD > **** > > Co 0 > SDD > F 1 1.00 > 0.1019000000D+01 0.1000000000D+01 > > > The first input file just seems to crash while the second gives me an error that stating there are no F atoms. > > Any help would be appreciated. > > Thanks, > Stephen George> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye{}crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Mon Jun 18 13:36:00 2012 From: "Adam Tenderholt atenderholt*o*gmail.com" To: CCL Subject: CCL:G: Gaussian ECP Message-Id: <-47099-120618122500-25036-bjC6uj7NpIFy8q5EzADyIw.@.server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=20cf3071c664d0628604c2c19a88 Date: Mon, 18 Jun 2012 09:24:28 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt[]gmail.com] --20cf3071c664d0628604c2c19a88 Content-Type: text/plain; charset=ISO-8859-1 Hi Stephen, Your first example looks like it should work, although the problem might be related to the number of spaces after your ECP definition. Does Gaussian care if you have more than one blank line at the end? Perhaps it doesn't like the Co basis set input, so maybe split it into two parts (note that I'm denoting the end and start of the file with ---): --- %chk=PBE0SDD %NProcShared=8 # gen pbe1pbe pseudo=read Molecule Name Atom Description C 0 6-31G** **** H 0 6-31G** **** N 0 6-31G** **** Si 0 6-31G** **** Co 0 SDD **** Co 0 F 1 1.00 0.1019000000D+01 0.1000000000D+01 **** Co 0 SDD --- As far as your second example, it should crash because you put f-block basis set information in with the definition of the psuedopotential. Adam --20cf3071c664d0628604c2c19a88 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Stephen,

Your first example looks like it should work= , although the problem might be related to the number of spaces after your = ECP definition. Does Gaussian care if you have more than one blank line at = the end? Perhaps it doesn't like the Co basis set input, so maybe split= it into two parts (note that I'm denoting the end and start of the fil= e with ---):

---
%chk=3DPBE0SDD
%NProcShared=3D8
# gen pbe1pbe ps= eudo=3Dread

Molecule Name

Atom Description

C 0
6-31G**
****<= /span>
H 0
6-31G**<= br style> ****
N 0
6-31G**
****
Si 0=
6-31G**
****
Co 0
SDD
****
Co 0
F 1 1.00
=A00.1019000000D+01 0.1000000000D+01
****

Co 0
SDD

---

As far= as your second example, it should crash because you put f-block basis set = information in with the definition of the psuedopotential.

Adam

--20cf3071c664d0628604c2c19a88-- From owner-chemistry@ccl.net Mon Jun 18 18:41:00 2012 From: "MarkG gates.mark{=}gmail.com" To: CCL Subject: CCL: multiple job in single input file Message-Id: <-47100-120618162137-18377-RhFH3EqNlvZQBgR1s3OyuQ=-=server.ccl.net> X-Original-From: MarkG Content-Type: multipart/alternative; boundary="4fdf8dc7_7724c67e_280" Date: Mon, 18 Jun 2012 16:21:27 -0400 MIME-Version: 1.0 Sent to CCL by: MarkG [gates.mark[#]gmail.com] --4fdf8dc7_7724c67e_280 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Have a question about running a second job after optimization in the same input file. With the input layout: ### %chk = check # 6-311** / b3lyp opt=(modredundant,maxcycle=200) Molecule Name Atom coords. B N1 N2 length F --Link1-- # 6-311++ / b3lyp sp geom=allcheck ### Will the second job (single point energy) using the second basis set and original checkpoint file still retain the frozen atom ?.. or would I need to specify this again in the second section again ? Thanks in advance, Mark -- Sent with Sparrow (http://www.sparrowmailapp.com/?sig) --4fdf8dc7_7724c67e_280 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

Hi 
Have a question about runnin= g a second job after optimization in the same input file. 
With the input layout:
=23=23=23


=
%chk =3D check
=23 6-311** / b3lyp opt=3D(modredunda= nt,maxcycle=3D200)

Molecule Name

<= /div>
Atom coords.

B N1 N2 length =46
<= div>
--Link1--
=23 6-311++ / b3lyp sp geom=3Dallc= heck



=23=23=23
Will the second job (single point energy) using the second basis s= et and original checkpoint file still retain the frozen atom =3F.. or wou= ld I need to specify this again in the second section again =3F

Thanks in advance,
Mark 



 
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--4fdf8dc7_7724c67e_280-- From owner-chemistry@ccl.net Mon Jun 18 19:57:00 2012 From: "Andrew Orry andy(-)molsoft.com" To: CCL Subject: CCL: 3D Molecules on the iPhone and iPad - iMolview New Version 1.5 Message-Id: <-47101-120618184852-18183-srxlf36j4ks5FWNxgT1EGA-,-server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 18 Jun 2012 15:53:24 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy[#]molsoft.com] Dear All, We have released a new version of iMolview (v1.5), please click here http://www.molsoft.com/iMolview.html for additional information. iMolview is an app that lets you browse protein, DNA, chemicals, and molecular documents in 3D on the iPhone and iPad. The key new features include: - support for high resolution retina display in iPad3 - simultaneous display of multiple proteins and superposition - side-by-side stereo - new tools for measuring and displaying distances and angles - export fully interactive chemical spreadsheets from ICM-Chemist http://www.molsoft.com/icm-chemist.html to the iPad (see screenshot: http://goo.gl/Fw7gw) iMolview is under active development and we would like to thank members of the CCL community for their feature requests. Thanks, Andrew -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 USA Tel: 858-625-2000 x108 Fax: 828-625-2888 -- www.molsoft.com www.twitter.com/molsoft From owner-chemistry@ccl.net Mon Jun 18 20:31:00 2012 From: "Andrew Yeung andrew.yeung^-^chem.tamu.edu" To: CCL Subject: CCL:G: multiple job in single input file Message-Id: <-47102-120618194605-12398-u4+fHzOCz0Y1+GXNA4dF2A*o*server.ccl.net> X-Original-From: Andrew Yeung Content-Type: multipart/alternative; boundary="------------020108000300010107040704" Date: Mon, 18 Jun 2012 18:45:55 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung+/-chem.tamu.edu] This is a multi-part message in MIME format. --------------020108000300010107040704 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Try the // syntax? http://www.gaussian.com/g_tech/g_ur/k_opt.htm "Compound Jobs. ... It is also common to follow an optimization with a single point energy calculation at a higher level of theory. The following route section automatically performs an HF/6-31G(d,p) optimization followed by an MP4/6-31G(d,p) single point energy calculation : # MP4/6-31G(d,p)//HF/6-31G(d,p) Test" Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-06-18 3:21 PM, MarkG gates.mark{=}gmail.com wrote: > > Hi > Have a question about running a second job after optimization in the > same input file. > With the input layout: > ### > > > %chk = check > # 6-311** / b3lyp opt=(modredundant,maxcycle=200) > > Molecule Name > > Atom coords. > > B N1 N2 length F > > --Link1-- > # 6-311++ / b3lyp sp geom=allcheck > > > > ### > Will the second job (single point energy) using the second basis set > and original checkpoint file still retain the frozen atom ?.. or would > I need to specify this again in the second section again ? > > Thanks in advance, > Mark > > > > -- > > Sent with Sparrow > --------------020108000300010107040704 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit
Try the // syntax?

http://www.gaussian.com/g_tech/g_ur/k_opt.htm

"Compound Jobs. ... It is also common to follow an optimization with a single point energy calculation at a higher level of theory. The following route section automatically performs an HF/6-31G(d,p) optimization followed by an MP4/6-31G(d,p) single point energy calculation :

# MP4/6-31G(d,p)//HF/6-31G(d,p) Test"

Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837
On 2012-06-18 3:21 PM, MarkG gates.mark{=}gmail.com wrote:

Hi 
Have a question about running a second job after optimization in the same input file. 
With the input layout:
###


%chk = check
# 6-311** / b3lyp opt=(modredundant,maxcycle=200)

Molecule Name

Atom coords.

B N1 N2 length F

--Link1--
# 6-311++ / b3lyp sp geom=allcheck



###
Will the second job (single point energy) using the second basis set and original checkpoint file still retain the frozen atom ?.. or would I need to specify this again in the second section again ?

Thanks in advance,
Mark 



 
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--------------020108000300010107040704-- From owner-chemistry@ccl.net Mon Jun 18 21:40:00 2012 From: "Billy McCann bwm0005*tigermail.auburn.edu" To: CCL Subject: CCL:G: Using read-write file to distribute time allocation Message-Id: <-47103-120618192251-17804-YwbSwoNz+p7tZK2GBp8YPw__server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 18 Jun 2012 23:22:38 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005(!)tigermail.auburn.edu] Dave, The read-write file can be used for time allocation, so to speak, in that an incomplete job can be restarted from the read-write file. This can be accomplished using the `Restart` keyword in your route line. See [1] for more details. Writing a script to resubmit every 24.5 hours may be an easy way to automate this, e.g. [pseudo-code] `while true; sleep 24.5 hrs ; if rwf.exists then resubmit else exit` (should you place %nosave after the %rwf line). If you'd like some help with the scripting, just post back. Happy to help. [1] http://www.gaussian.com/g_tech/g_ur/k_restart.htm Hope that helps. Billy Wayne +++++++++++++++++++++++++ Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Reseach Auburn University, Alabama Office # = 334.844.6948 bwayne on irc.freenode.net +++++++++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu~!~ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu~!~ccl.net] On Behalf Of Davee McCloud davemccloud886:yahoo.com Sent: Saturday, June 16, 2012 3:38 PM To: Billy McCann Subject: CCL: Using read-write file to distribute time allocation Sent to CCL by: "Davee McCloud" [davemccloud886::yahoo.com] Dear All: I am aware that rwf can be used to segment memory allocation. However, I will like to know if this can also be used in time allocation/distribution on a server e.g. I am submitting a job to a server that only allows 24 hour allocation,I am sure my job will require more than 24 hours, can i write a rwf for time allocation so my job does not automatically stop after 24 hours? Thanks Dave McCloudhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt