From owner-chemistry@ccl.net Sat Aug 25 00:17:00 2012 From: "John Keller jwkeller]_[alaska.edu" To: CCL Subject: CCL: IQmol (Win 7) crashes opening a QChem 4.0 output.out file Message-Id: <-47461-120825001136-21270-tgcPs67quQpsv+1k6xuA2w^server.ccl.net> X-Original-From: "John Keller" Date: Sat, 25 Aug 2012 00:11:34 -0400 Sent to CCL by: "John Keller" [jwkeller..alaska.edu] My IQmol 2.0.1 application for Win 7 can open Q-Chem 4.0 Test.Fchk files and display MO surfaces, etc., however it crashes whenever I try to open an output.out file from any type of Q-Chem opt, freq, or SP job. These jobs run successfully according to the output.out text, and they are processed correctly by WebMO, so why can't IQmol handle them? Has anyone else had this problem, or know a work-around? (I posted this question at www.iqmol.org too, but have not heard back yet.) John Keller jwkeller:alaska.edu Dept of Chemistry & Biochemistry University of Alaska Fairbanks From owner-chemistry@ccl.net Sat Aug 25 02:34:00 2012 From: "quantum chem qchem66(!)gmail.com" To: CCL Subject: CCL:G: curve drawing Message-Id: <-47462-120825023233-22519-gnj+5L9ixXE0dGg0NMHGlQ[#]server.ccl.net> X-Original-From: "quantum chem" Date: Sat, 25 Aug 2012 02:32:32 -0400 Sent to CCL by: "quantum chem" [qchem66[*]gmail.com] Dear Members, I shall be thankful if someone helps me out in drawing/plotting the following. Comparative spectra theoretically obtained by Gaussian 09 and experimentally obtained spectra in a single figure one on top of the other.How this is done?Is there any software for this or we have to do some manual work. Thanks in advance QC From owner-chemistry@ccl.net Sat Aug 25 13:42:00 2012 From: "Saurabh sschitnis]~[gmail.com" To: CCL Subject: CCL:G: curve drawing Message-Id: <-47463-120825125703-9556-XFmqvb1kHyxRkJjJwGaucQ]_[server.ccl.net> X-Original-From: Saurabh Content-Type: multipart/alternative; boundary=f46d0444ed85faeb8804c819fabd Date: Sat, 25 Aug 2012 09:56:57 -0700 MIME-Version: 1.0 Sent to CCL by: Saurabh [sschitnis],[gmail.com] --f46d0444ed85faeb8804c819fabd Content-Type: text/plain; charset=ISO-8859-1 Dear QC, Gaussview can create a spectrum by interpolating between calculated frequencies. You can then export the spectrum as an x,y table and plot it using your favourite program. In Gaussview, open up the logfile which has the calculated frequencies (remember to use freq=raman in your routecard if you need the raman spectrum). Then go to Results>Vibrations>Click on Spectrum and you will see the IR and/or raman spectrum created by Gaussian using frequencies in the log file. You can right click anywhere on the spectrum and adjust scaling and zoom. You can also right click and either Export the spectrum as an image file, or save it as an x,y table in a text file, which can be opened by excel or other programs like it. (For Excel, File>Import the file text file>separate into columns by space or comma delimiters). You might have to play around with the Stepsize variable in the Save Data window to get something that matches your experimental spectrum. cheers Saurabh On Fri, Aug 24, 2012 at 11:32 PM, quantum chem qchem66(!)gmail.com < owner-chemistry(-)ccl.net> wrote: > > Sent to CCL by: "quantum chem" [qchem66[*]gmail.com] > Dear Members, > I shall be thankful if someone helps me out in > drawing/plotting the following. > Comparative spectra theoretically obtained by Gaussian 09 and > experimentally > obtained spectra in a single figure one on top of the other.How this is > done?Is > there any software for this or we have to do some manual work. > Thanks in advance > QC> > --f46d0444ed85faeb8804c819fabd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear QC,

Gaussview can create a spectrum by interpolatin= g between calculated frequencies. You can then export the spectrum as an x,= y table and plot it using your favourite program.=A0

In Gaussview, open up the logfile which has the calculated frequencies (rem= ember to use freq=3Draman in your routecard if you need the raman spectrum)= . Then go to Results>Vibrations>Click on Spectrum and you will see th= e IR and/or raman spectrum created by Gaussian using frequencies in the log= file. You can right click anywhere on the spectrum and adjust scaling and = zoom. You can also right click and either Export the spectrum as an image f= ile, or save it as an x,y table in a text file, which can be opened by exce= l or other programs like it. (For Excel, File>Import the file text file&= gt;separate into columns by space or comma delimiters).

You might have to play around with the Stepsize variabl= e in the Save Data window to get something that matches your experimental s= pectrum.

cheers
Saurabh

On Fri, Aug 24, 2012 at 11:32 PM, quantum chem qchem66(!)gmail.com <owner-chemistry(-)ccl.net> wro= te:

Sent to CCL by: "quantum =A0chem" [qchem66[*]gmail.com]
Dear Members,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I shall be thankful if someone helps me = out in
drawing/plotting the following.
Comparative spectra theoretically obtained by Gaussian 09 and experimentall= y
obtained spectra in a single figure one on top of the other.How this is don= e?Is
there any software for this or we have to do some manual work.
Thanks in advance
QC



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--f46d0444ed85faeb8804c819fabd-- From owner-chemistry@ccl.net Sat Aug 25 17:02:00 2012 From: "Amir Bernat bernat . post.bgu.ac.il" To: CCL Subject: CCL:G: curve drawing Message-Id: <-47464-120825162205-15678-8iaFO7EhnfK6uSQkHaYeWQ,,server.ccl.net> X-Original-From: Amir Bernat Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 25 Aug 2012 22:21:57 +0200 MIME-Version: 1.0 Sent to CCL by: Amir Bernat [bernat|*|post.bgu.ac.il] HI QC Do you need to calculate IR, Raman or stimulated Raman spectra? in general you need to extract the vibration location and intensity (in stimulated raman you have to calculate it from the activity), use a scale factor appropriate to your calculations and then plot each mode with it's line broadening function (Lorentzian and/or Gaussian) to fit the line width of your experiment. This can be done in a verity of programs, Matlab / origin and even Excel. In the Gaussian .out file look for this section: Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A A A Frequencies -- 40.0361 81.4720 132.8084 Red. masses -- 3.7973 4.1456 2.4983 Frc consts -- 0.0036 0.0162 0.0260 IR Inten -- 1.3229 0.7867 3.7615 Raman Activ -- 3.1025 3.1208 0.9311 Depolar (P) -- 0.7403 0.7336 0.6794 Depolar (U) -- 0.8507 0.8463 0.8091 Amir On Sat, Aug 25, 2012 at 6:56 PM, Saurabh sschitnis]~[gmail.com wrote: > Dear QC, > > Gaussview can create a spectrum by interpolating between calculated > frequencies. You can then export the spectrum as an x,y table and plot it > using your favourite program. > > In Gaussview, open up the logfile which has the calculated frequencies > (remember to use freq=raman in your routecard if you need the raman > spectrum). Then go to Results>Vibrations>Click on Spectrum and you will see > the IR and/or raman spectrum created by Gaussian using frequencies in the > log file. You can right click anywhere on the spectrum and adjust scaling > and zoom. You can also right click and either Export the spectrum as an > image file, or save it as an x,y table in a text file, which can be opened > by excel or other programs like it. (For Excel, File>Import the file text > file>separate into columns by space or comma delimiters). > > You might have to play around with the Stepsize variable in the Save Data > window to get something that matches your experimental spectrum. > > cheers > Saurabh > > On Fri, Aug 24, 2012 at 11:32 PM, quantum chem qchem66(!)gmail.com > wrote: >> >> >> Sent to CCL by: "quantum chem" [qchem66[*]gmail.com] >> Dear Members, >> I shall be thankful if someone helps me out in >> drawing/plotting the following. >> Comparative spectra theoretically obtained by Gaussian 09 and >> experimentally >> obtained spectra in a single figure one on top of the other.How this is >> done?Is >> there any software for this or we have to do some manual work. >> Thanks in advance >> QC>> E-mail to subscribers: CHEMISTRY/./ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or use>> > -- -- Amir Bernat http://physweb.bgu.ac.il/~bernat/ From owner-chemistry@ccl.net Sat Aug 25 20:58:01 2012 From: "Guenter Grethe ggrethe###att.net" To: CCL Subject: CCL: Call for Applications----CINF-Accelrys Scholarships Message-Id: <-47465-120825182619-15859-Xz6VXRcPom54T6vxWSY95g]*[server.ccl.net> X-Original-From: "Guenter Grethe" Date: Sat, 25 Aug 2012 18:26:18 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe\a/att.net] CINF Scholarship for Scientific Excellence Sponsored by Accelrys The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by Accelrys is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to two scholarships valued at $1,000 each will be presented at the 245th ACS National Meeting in New Orleans, LA, April 7 11, 2013. Applicants must be enrolled at a certified college or university and must present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe..att.net, that you are applying for a scholarship. Submit your abstract at http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program in the session CINF Scholarship for Scientific Excellence. PACS will be open for abstract submissions on August 20, 2012, and close on October 15, 2012. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by January 31, 2013. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of Accelrys-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe ggrethe..att.net From owner-chemistry@ccl.net Sat Aug 25 22:15:00 2012 From: "Nguyen Minh Ly nguyenminhly2209/a\yahoo.com" To: CCL Subject: CCL:G: Graphed by Gaussian Message-Id: <-47466-120825221421-22862-y85jtW8BuKrpqiQ2NGqXtg%server.ccl.net> X-Original-From: "Nguyen Minh Ly" Date: Sat, 25 Aug 2012 22:14:19 -0400 Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209]![yahoo.com] Dear sir, I'm Ly, Viet Nam I have made a few chemical experiments. So I have a few parameters which need represented by a graph. For example: I made a chemical reaction between Mg and HCl solution. I read the volume of H2 gas which produced every 15 seconds. I need to draw a graph to represent the change in volume of H2 gas. I can still do this with Excel. But I want to draw the graph with Gaussian 03. Can you tell me how to do this by Gaussian ? Thanks for your helping.