From owner-chemistry@ccl.net Tue Aug 1 09:46:00 2006 From: "Shobe, David dshobe(!)sud-chemieinc.com" To: CCL Subject: CCL:G: C70 nanotube Message-Id: <-32321-060801094442-26604-gl69Iuwl/7JvsYOAvDJ0tg---server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 1 Aug 2006 15:44:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe^^^sud-chemieinc.com] First, just in case you're new to this: The error message you received indicates that self-consistency of the B3LYP wave function was not reached. It has nothing to do with optimization of the geometry. As for fixing the problem: (1) simply increasing the number of SCF cycles is likely to help in this case, since I think molecule size is your major problem. Even scf(maxcyc=9999) might not be excessive for a pi-conjugated 70-atom system. (2) try the optimization as a single point and without scf=tight. If you get a converged wave function then, you can use scf=tight guess=read to refine that wave function. (3) if (1) and (2) don't work try scf=(qc,maxcyc=9999). The qc option is an instruction to use a different algorithm for the calculation. To the list: I'm assuming here that C70 is not a multi-reference problem, but simply a more difficult than usual single-reference-approximation problem. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry(_)ccl.net [mailto:owner-chemistry(_)ccl.net] Sent: Monday, July 31, 2006 7:53 PM To: Shobe, David Subject: CCL:G: C70 nanotube Sent to CCL by: "Mike Miller" [mill(0)pica.army.mil] Dear colleagues, I was provided the output of a semi-empirical PM3 optimization (z-matrix) of a C70 nanotube. I am now trying to run it using Gaussian 03 Rev.c.02, B3LYP/6-31g(d). It will not optimize, so I ran a single point energy calculation- same problems encountered; here is a summary: First calculation performed: T Opt B3LYP/6-31g(d) SCF=tight Results: Convergence criterion not met. E(RB+HF-LYP) = -2665.81029984 Convergence failure -- run terminated Second calculation performed: T B3LYP/6-31g(d) SCF=tight Results: Convergence criterion not met. E(RB+HF-LYP) = -2665.81029979 Convergence failure -- run terminated I don't know what the problem is, however, I see two ways to proceed... find a database of z-matrices of nanotubes and compare my z-matrix to that and go from there... or if there is something about the Gaussian program that I have to tweak in order to get the optimization to work. Any assistance would be appreciated. Mikehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. 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From owner-chemistry@ccl.net Tue Aug 1 10:21:00 2006 From: "IEJMD iejmd%x%yahoo.com" To: CCL Subject: CCL: Call for papers: European Symposium on Computer Aided Process Engineering Message-Id: <-32322-060731194927-26719-f/yADe7xi0JBjyOD3bd2vw!^!server.ccl.net> X-Original-From: IEJMD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 31 Jul 2006 15:49:23 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: IEJMD [iejmd.:.yahoo.com] Call for papers: European Symposium on Computer Aided Process Engineering ESCAPE 17 17th European Symposium on Computer Aided Process Engineering 27 - 30 May 2007, Bucharest, ROMANIA Send registration to: iejmd]^[yahoo.com ESCAPE 17 Program ----------------- Modelling in Computer Aided Process Engineering – new horizons -Multi-scale modelling – from molecular to whole sites -System identification -Applied numerical methods -CFD and innovative equipment design -Computational chemistry and thermodynamics -Improving modelling & simulation with new computational approaches including grid computing, clusters, component technology, services & operability -Artificial intelligence including agents, data mining, machine learning, fault diagnosis, evolutionary computing Products and processes – design fundamentals -From product properties to molecular design -Nanoscale processes and materials -New or improved process synthesis design -Integrated process and product design -CAPE for oil & gas processes -CAPE – industrial success stories Optimisation and optimal process control and operation -Planning, scheduling and distributed control systems -System diagnosis and management of supply chain -Hierarchical and optimal process control -Control-oriented integrated design Systems biology and biological processes -Bioproducts and biomaterials -Drug design and controlled release -Systems biology and modelling of metabolic processes -Integrated databases and cell process simulators Process integration and sustainable development -Process intensification -Combined heat and power site-level integration -Life cycle modelling -Safety analysis, risk assessment, and environmental impact -Bio diesel and sustainable fuels -Waste management Send abstract as Word file to: iejmd]^[yahoo.com Abstracts with approximately 500 words written in English should contain title, authors, affiliations, address, keywords and the preferred theme/track. Abstracts will be reviewed and selected by the Scientific Committee. On notification of acceptance, authors will be asked to submit a paper which will be fully refereed. At least one of the authors will be required to present the accepted paper in person at the symposium. Proceedings All accepted papers will be published in the symposium proceedings as a volume of the book series on Computer Aided Chemical Engineering, published by Elsevier Science B.V. These proceedings will be distributed to all symposium participants. Best regards, Ovidiu Ivanciuc ###################### Ovidiu Ivanciuc Sealy Center for Structural Biology and Molecular Biophysics Department of Biochemistry and Molecular Biology University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-0857 USA Email: oiivanci]^[utmb.edu Email: iejmd]^[yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Tue Aug 1 11:34:00 2006 From: "Gianluca Santarossa gianluca.santarossa###chem.ethz.ch" To: CCL Subject: CCL: How to make a movie from the trajectory file at Cerius2? Message-Id: <-32323-060801051528-25880-BtDTh5VEM6DS1zO811ALQw_-_server.ccl.net> X-Original-From: "Gianluca Santarossa" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=iso-8859-1 Date: Tue, 01 Aug 2006 10:27:53 +0200 MIME-Version: 1.0 Sent to CCL by: "Gianluca Santarossa" [gianluca.santarossa-#-chem.ethz.ch] On Tue, 01 Aug 2006 02:58:56 +0200, Jun Zhao jzhao#,#tamu.edu wrote: > Sent to CCL by: "Jun Zhao" [jzhao|-|tamu.edu] > Does anyone know how to make a movie from the trajectory file? I got the > trajectory file from the molecular dynamics simulation at Cerius 2. I don't know Cerius, but if you can easily generate snapshots from your trajectory you can make the movie using mencoder, which you can download from: http://www.mplayerhq.hu/ This is a simple example: mencoder "mf://*.jpg" -mf fps=25 -o output.avi -ovc lavc -lavcopts vcodec=mpeg4 For all the other options refer to mencoder documentation. Regards, Gianluca -- Gianluca Santarossa Institute for Chemical and Bioengineering Department of Chemistry and Applied Biosciences ETH Zurich, Hönggerberg, HCI, 8093 Zurich Phone: +41 44 633 4232 Fax: +41 44 633 1163 E-Mail: gianluca.santarossa[a]chem.ethz.ch From owner-chemistry@ccl.net Tue Aug 1 12:09:00 2006 From: "Bingbing Suo bingsuo.ccl[#]gmail.com" To: CCL Subject: CCL:G: C70 nanotube Message-Id: <-32324-060731221920-21696-l011Mc1jAF13UcHtYYNnCg|-|server.ccl.net> X-Original-From: "Bingbing Suo" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Mon, 31 Jul 2006 18:16:05 -0800 Mime-Version: 1.0 Sent to CCL by: "Bingbing Suo" [bingsuo.ccl]|[gmail.com] It seems the SCF calculation is not convergence. Try to use scf(MaxCycle=100) which changes the maximum cycles of SCF iteration to 100(you can choose a larger value) from default value 64. If the single point calculation can be done, then optimize C70 structure. I hope it will work. Sincerely, Bing Suo >Sent to CCL by: "Mike Miller" [mill(0)pica.army.mil] >Dear colleagues, >I was provided the output of a semi-empirical PM3 optimization (z-matrix) of a C70 nanotube. I am now trying to run it using Gaussian 03 Rev.c.02, B3LYP/6-31g(d). It will not optimize, so I ran a single point energy calculation- same problems encountered; here is a summary: > >First calculation performed: >T Opt B3LYP/6-31g(d) SCF=tight > >Results: >Convergence criterion not met. >E(RB+HF-LYP) = -2665.81029984 >Convergence failure -- run terminated > > >Second calculation performed: >T B3LYP/6-31g(d) SCF=tight > >Results: >Convergence criterion not met. >E(RB+HF-LYP) = -2665.81029979 >Convergence failure -- run terminated > >I don't know what the problem is, however, I see two ways to proceed... find a database of z-matrices of nanotubes and compare my z-matrix to that and go from there... or if there is something about the Gaussian program that I have to tweak in order to get the optimization to work. > >Any assistance would be appreciated. >Mike> > > From owner-chemistry@ccl.net Tue Aug 1 12:43:00 2006 From: "Zhao, Jun jzhao .. tamu.edu" To: CCL Subject: CCL: How to make a movie from the trajectory file at Cerius2? Message-Id: <-32325-060801013524-10298-hn6Mm5GcMEgzcs3TqPSQBQ[*]server.ccl.net> X-Original-From: "Zhao, Jun" Date: Tue, 1 Aug 2006 04:59:37 -0000 Sent to CCL by: "Zhao, Jun" [jzhao]![tamu.edu] That is helpful. Thank you. "huanglei huanglei%%mail.utexas.edu" said: > Sent to CCL by: "huanglei" [huanglei^mail.utexas.edu] > Hi, Jun > > Generally I use vmd to generate a movie based on pdb file. You > can write a program or use existing code to tranform the trajectory > in other format into pdb. Good luck. > > Best regards, > lei > > > > > ======= 2006-07-31 18:58:25 ======= > > >Sent to CCL by: "Jun Zhao" [jzhao|-|tamu.edu] > >Does anyone know how to make a movie from the trajectory file? I got the trajectory file from the molecular dynamics simulation at Cerius 2. I want to make a short movie based on the trajectory file so that I can play it in the powerpoint presentation. Any suggestion is greatly appreciated. > > > >Jun Zhao > > > >Ph.D. Candidate > >Dept of Atmospheric Sciences > >Texas A&M University > >College Station, TX 77843 > >Office: (979) 458-0555 > >Fax: (979) 862-4466> > > > -- Jun Zhao From owner-chemistry@ccl.net Tue Aug 1 13:19:01 2006 From: "Elaine Meng meng]_[cgl.ucsf.edu" To: CCL Subject: CCL: How to make a movie from the trajectory file at Cerius2? Message-Id: <-32326-060801125800-9042-ZJlsyfeNbMsydqnUonUZig(!)server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 1 Aug 2006 12:57:59 -0400 Sent to CCL by: "Elaine Meng" [meng() cgl.ucsf.edu] Hi Jun, I don't know what format is created by Cerius2, but you can make movies from trajectories in several common formats using Chimera. The "MD Movie" tool replays the trajectory, and choosing "File... Record movie" > from that tool allows you to specify frame-saving and movie-encoding options. It will automatically assemble the movie in the specified format (Quicktime, AVI, MPEG, others) which can then be imported into PowerPoint. Here is the man page for MD Movie: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html and from there, choose the "Recording a movie" link to see the part about creating movies. There is also a tutorial in which a movie is made from a trajectory: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html Chimera can be downloaded from http://www.cgl.ucsf.edu/chimera/download.html I recommend version 1.2255 (newer, lower in the download page) because it has the most recent improvements in movie saving. I hope this helps, Elaine From owner-chemistry@ccl.net Tue Aug 1 14:48:00 2006 From: "Tapas Kar tapaskar^^cc.usu.edu" To: CCL Subject: CCL:G: C70 nanotube Message-Id: <-32327-060801144611-10214-mDuARxOM/hGAxZK2BlgRJg{}server.ccl.net> X-Original-From: "Tapas Kar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 1 Aug 2006 12:45:19 -0600 MIME-Version: 1.0 Sent to CCL by: "Tapas Kar" [tapaskar\a/cc.usu.edu] There may be energy oscillation - to know how energy is changing in scf cycles, please use #P option in route card. Then "grep Delta-E output-file name" to print energies. -----Original Message----- > From: owner-chemistry ~ ccl.net [mailto:owner-chemistry ~ ccl.net] Sent: Tuesday, August 01, 2006 10:20 AM To: Kar, Tapas Subject: CCL:G: C70 nanotube Sent to CCL by: "Bingbing Suo" [bingsuo.ccl]|[gmail.com] It seems the SCF calculation is not convergence. Try to use scf(MaxCycle=100) which changes the maximum cycles of SCF iteration to 100(you can choose a larger value) from default value 64. If the single point calculation can be done, then optimize C70 structure. I hope it will work. Sincerely, Bing Suo >Sent to CCL by: "Mike Miller" [mill(0)pica.army.mil] >Dear colleagues, >I was provided the output of a semi-empirical PM3 optimization (z-matrix) of a C70 nanotube. I am now trying to run it using Gaussian 03 Rev.c.02, B3LYP/6-31g(d). It will not optimize, so I ran a single point energy calculation- same problems encountered; here is a summary: > >First calculation performed: >T Opt B3LYP/6-31g(d) SCF=tight > >Results: >Convergence criterion not met. >E(RB+HF-LYP) = -2665.81029984 >Convergence failure -- run terminated > > >Second calculation performed: >T B3LYP/6-31g(d) SCF=tight > >Results: >Convergence criterion not met. >E(RB+HF-LYP) = -2665.81029979 >Convergence failure -- run terminated > >I don't know what the problem is, however, I see two ways to proceed... find a database of z-matrices of nanotubes and compare my z-matrix to that and go from there... or if there is something about the Gaussian program that I have to tweak in order to get the optimization to work. > >Any assistance would be appreciated. >Mikehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt