From owner-chemistry@ccl.net Thu Oct 20 06:55:00 2005 From: "may abdelghani may01dz**yahoo.fr" To: CCL Subject: CCL: The x,y,z coordinat of porphyrins Message-Id: <-29667-051020064659-21481-eSc6C2yCCSce8pLLLmWjCA|a|server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 20 Oct 2005 11:46:52 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz*yahoo.fr] Dear CLLers, > From were I Can, my CClers friend, find (or obtain) the (X, Y, Z) coordinate of anionic (H2TSPP and NiTCPP) porphyrins Thanks ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Téléchargez cette version sur http://fr.messenger.yahoo.com From owner-chemistry@ccl.net Thu Oct 20 08:00:00 2005 From: "Alexander Martins Silva alex.msilva##uol.com.br" To: CCL Subject: CCL: Gaussian parallel Message-Id: <-29668-051020075922-12132-jfV6tO3fFToEnzxvQTowRw*|*server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Oct 2005 09:59:22 +0000 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva ~ uol.com.br] Hi, I've compiled a parallel version of Gaussian with Linda and I'm trying to execute a parallel test job at my cluster, but I get only a serial job on the master node. The configuration is ok: I've compiled the Gaussian with PGF77, the Linda installation have created a linda-exe dir com *.exel files: $ls -ls /usr/local/g03/linda-exe/ total 16 1 lrwxrwxrwx 1 root users 14 Out 18 15:56 l1002.exe -> ../linda-dummy* 1 lrwxrwxrwx 1 root users 13 Out 18 15:56 l1002.exel -> ../l1002.exel* 1 lrwxrwxrwx 1 root users 14 Out 18 15:56 l1014.exe -> ../linda-dummy* 1 lrwxrwxrwx 1 root users 13 Out 18 15:56 l1014.exel -> ../l1014.exel* 1 lrwxrwxrwx 1 root users 14 Out 18 15:56 l1101.exe -> ../linda-dummy* 1 lrwxrwxrwx 1 root users 13 Out 18 15:56 l1101.exel -> ../l1101.exel* (...); %nprocl=nnodes is at the top of the input; and setenv GAUSS_LFLAGS '-vv -nodelist="node1 node2 ..."' What's the problem and how can I fix it? Thanks, Alexander. From owner-chemistry@ccl.net Thu Oct 20 09:31:00 2005 From: "Valentin Ananikov val-*-ioc.ac.ru" To: CCL Subject: CCL: Stereo 3D Displays & Equipment Message-Id: <-29669-051020092556-2934-xgQerptwZafiYhuM//eGFg,server.ccl.net> X-Original-From: Valentin Ananikov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 20 Oct 2005 17:19:25 +0400 MIME-Version: 1.0 Sent to CCL by: Valentin Ananikov [val]=[ioc.ac.ru] If somebody has an experience using 3D displays in solving computational chemistry problems, it would be useful to know a feedback. What practical help 3D displays can provide to modern computational chemistry? Does it speed up building models, analyzing results or help in something else? I am mostly interesting in pragmatic point of view (of course, 3D images are very useful to awake imagination, impress students, art, etc.). Best regards, Valentin Ananikov. > Sent to CCL by: "Warren DeLano" [warren\a/delsci.com] > > Here is some current information for those of you ordering yourself a > new "Quad" Quadro-based Mac for doing Stereo 3D visualization. You will > need a good CRT display, a stereo signal emitter, and shutter glasses. > > Stereo 3D glasses & emitters: > > - More expensive: StereoGraphics > l> > > - Less expensive: NuVision3D > > > Thanks to LCD dominance, it is getting mucher harder to find a good CRT > display. You may need to hunt around a bit or buy "pre-owned". > > The critical monitor specifications for Stereo 3D are: > > - Must be a CRT (not an LCD). > - Should be as big as you can afford (20-22"). > - HD15 VGA input (DVI is very rare). > - Vertical refresh must be at least 120 Hz. > - Horizontal sync frequency must be at least 130 kHz (ideally 140 kHz). > > Note that the last point is CRITICAL. Do not buy a CRT monitor for > stereo 3D until you have confired that it can do a horizontal sync of at > least 130 kHz. Beware of consumer monitors have horizontal sync limits > of 80-120 kHz and thus cannot do stereo well. > > Good stereo-capable CRT displays that are still available NEW: > > - Philips 202P73 > > 74> > > - Iiyama Vision Master Pro 514 / HM204DT > > > Good discontinued stereo-capable displays (buy USED on eBay, etc.): > > - IBM ThinkVision C220p > - HP p1230 CRT Monitor (P9613W) > - DELL p1230 > - Sony GDM-C520K > - NEC FP2141SB-BK > - NEC-Mitsubishi Diamond Pro 2070SB-BK > - Sun X7149A > > Borderline displays: > > - ViewSonic, P225FB (H-sync: 127 kHz - good for 1280x960 _+_ ~110 Hz) > - Samsung SyncMaster 1100 DF (H-sync: 121 kHz) > - Sun X7149A (H-sync: 121 kHz) > > Unsuitable displays: > > - ViewSonic G220f/fb, G810, G90f/fb > - Philips 201B40, 201B45 > - NEC Accusync 120 > - Mitsubishi Diamond Pro 930SB > - Samsung SyncMaster 1000 P, 997DF/997MB > > See: http://monitors.alege.net for info on tons of monitors, old & new. > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:warren_+_delsci.com> > > From owner-chemistry@ccl.net Thu Oct 20 10:57:00 2005 From: "Perry E. Metzger perry**piermont.com" To: CCL Subject: CCL: Stereo 3D Displays & Equipment Message-Id: <-29670-051020104546-25536-2oXbOm0F2aQkF6fXxgessg[-]server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Thu, 20 Oct 2005 10:45:44 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry*|*piermont.com] "Valentin Ananikov val-*-ioc.ac.ru" writes: > If somebody has an experience using 3D displays in solving computational > chemistry problems, it would be useful to know a feedback. > > What practical help 3D displays can provide to modern computational > chemistry? > > Does it speed up building models, analyzing results or help in > something else? > > I am mostly interesting in pragmatic point of view (of course, 3D images > are very useful to awake imagination, impress students, art, etc.). Having worked in other context with stereographic imaging systems, let me say that if you are working on large objects with complicated shape, nothing is going to give you better intuition about what they are *really* like than seeing them in 3D. I would imagine that for many people who are dealing with things like biological machines (there are more in the world than just the ribosome and ATP synthase), this sort of thing would be invaluable, but lets say you just wanted to get a better intuitive understanding of how a particular catalyst might work? Additionally, 3D displays give you a lot of extra ability to work with tabular information, graphs, etc. There are a lot of new possibilities for visualizing complex functions, multiple analysis runs, etc., etc. in three dimensions. There is nothing quite like *seeing* for humans. We are highly visual creatures -- we spend an enormous percentage of our brain's energy budget on our visual systems. Exploiting these brain systems is a key tool in building understanding. Perry From owner-chemistry@ccl.net Thu Oct 20 11:32:00 2005 From: "Warren DeLano warren-.-delsci.com" To: CCL Subject: CCL: Stereo 3D Displays & Equipment Message-Id: <-29671-051020111705-6519-sWg8F8a/77EqIElgG4L4Xw-x-server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 20 Oct 2005 08:17:37 -0700 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren() delsci.com] Though stereo 3D displays are by no means a panacea, they can be helpful when visualizing complex three dimensional structures and interactions where no single 2D projection can convey the complete picture. Stereo is much more useful visualizing macromolecules than small molecules (alone). Especially: - building macromolecular structures into experimental electron density. - visualizing protein/ligand interactions in buried cavities. - visualizing dynamic systems (e.g. MC, MD, structure or reaction "morphing"). - manual homology modeling from multiple superimposed templates - for teaching students who still think of molecules in 2D "ChemDraw" terms, or worse, 1D sequences. Improved graphics software over the past 10 years have certainly reduced the need for stereo 3D through use of surfaces, slices, and semantic coloring. But in personal pragmatic terms, I still find that stereo 3D provides my brain with more information in less time than any other visualization technique. However, more information isn't a good thing unless you can apply it effectively! Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren!A!delsci.com > -----Original Message----- > From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] > Sent: Thursday, October 20, 2005 7:35 AM > To: Warren DeLano > Subject: CCL: Stereo 3D Displays & Equipment > > > Sent to CCL by: Valentin Ananikov [val]=[ioc.ac.ru] > > If somebody has an experience using 3D displays in solving > computational chemistry problems, it would be useful to know a > feedback. > > What practical help 3D displays can provide to modern computational > chemistry? > > Does it speed up building models, analyzing results or help in > something else? > > I am mostly interesting in pragmatic point of view (of course, 3D > images are very useful to awake imagination, impress students, art, > etc.). > > Best regards, > Valentin Ananikov. > > > > Sent to CCL by: "Warren DeLano" [warren\a/delsci.com] > > > > Here is some current information for those of you ordering > yourself a > > new "Quad" Quadro-based Mac for doing Stereo 3D visualization. You > > will need a good CRT display, a stereo signal emitter, and > shutter glasses. > > > > Stereo 3D glasses & emitters: > > > > - More expensive: StereoGraphics > > > > tm > > l> > > > > - Less expensive: NuVision3D > > > > > > Thanks to LCD dominance, it is getting mucher harder to find a good > > CRT display. You may need to hunt around a bit or buy "pre-owned". > > > > The critical monitor specifications for Stereo 3D are: > > > > - Must be a CRT (not an LCD). > > - Should be as big as you can afford (20-22"). > > - HD15 VGA input (DVI is very rare). > > - Vertical refresh must be at least 120 Hz. > > - Horizontal sync frequency must be at least 130 kHz > (ideally 140 kHz). > > > > Note that the last point is CRITICAL. Do not buy a CRT monitor for > > stereo 3D until you have confired that it can do a > horizontal sync of > > at least 130 kHz. Beware of consumer monitors have horizontal sync > > limits of 80-120 kHz and thus cannot do stereo well. > > > > Good stereo-capable CRT displays that are still available NEW: > > > > - Philips 202P73 > > > > > > 45 > > 74> > > > > - Iiyama Vision Master Pro 514 / HM204DT > > > > > > Good discontinued stereo-capable displays (buy USED on eBay, etc.): > > > > - IBM ThinkVision C220p > > - HP p1230 CRT Monitor (P9613W) > > - DELL p1230 > > - Sony GDM-C520K > > - NEC FP2141SB-BK > > - NEC-Mitsubishi Diamond Pro 2070SB-BK > > - Sun X7149A > > > > Borderline displays: > > > > - ViewSonic, P225FB (H-sync: 127 kHz - good for 1280x960 > _+_ ~110 Hz) > > - Samsung SyncMaster 1100 DF (H-sync: 121 kHz) > > - Sun X7149A (H-sync: 121 kHz) > > > > Unsuitable displays: > > > > - ViewSonic G220f/fb, G810, G90f/fb > > - Philips 201B40, 201B45 > > - NEC Accusync 120 > > - Mitsubishi Diamond Pro 930SB > > - Samsung SyncMaster 1000 P, 997DF/997MB > > > > See: http://monitors.alege.net for info on tons of > monitors, old & new. > > > > Cheers, > > Warren > > > > -- > > Warren L. DeLano, Ph.D. > > Principal Scientist > > > > . DeLano Scientific LLC > > . 400 Oyster Point Blvd., Suite 213 > > . South San Francisco, CA 94080 USA > > . Biz:(650)-872-0942 Tech:(650)-872-0834 > > . Fax:(650)-872-0273 Cell:(650)-346-1154 . > > mailto:warren_+_delsci.com> > > > From owner-chemistry@ccl.net Thu Oct 20 12:07:00 2005 From: "Alexander Martins Silva alex.msilva[*]uol.com.br" To: CCL Subject: CCL: Gaussian parallel starts... Message-Id: <-29672-051020113449-12667-6wLar54wKAFuGwz0cmMrTQ_+_server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Oct 2005 13:34:55 +0000 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva-$-uol.com.br] Hi, I was trying to execute a parallel job with Gaussian. The job starts but not run at the nodes. After g03l inputefile: $ g03l 453.inp & setenv GAUSS_EXEDIR /usr/local/g03/linda-exe:/usr/local/g03/bsd:/usr/local/g03/private:/usr/local/g03 g03 453.inp [2] 18731 $ ntsnet: using global map file "/usr/local/g03/linda7.1/intel-linux2.4-rh8/../common/lib/tsnet.map" ntsnet: couldn't find user map file "/home/alex/.tsnet.map" ntsnet: checking for /usr/local/g03/linda-exe/l302.exel ntsnet: using executable file /usr/local/g03/linda-exe/l302.exel ntsnet: maxlicense is 1000000 ******************************************** appl config file: /usr/local/g03/linda-exe/tsnet.config-l302_exel user config file: /home/alex/.tsnet.config global config file: /usr/local/g03/linda7.1/intel-linux2.4-rh8/../common/lib/tsnet.config user map file: /home/alex/.tsnet.map global map file: /usr/local/g03/linda7.1/intel-linux2.4-rh8/../common/lib/tsnet.map local node: at1 remote nodes: at1101 at1102 at1103 at1104 nodelist: at1101 at1102 at1103 at1104 nodefile: tsnet.nodes minwait: 600 maxwait: 600 workerwait: 900 masterload: 1.000000 workerload: 1.000000 fallbackload: 0.990000 maxprocspernode: 1 delay: 0 maxnodes: Number of available nodes minworkers: 3 maxworkers: 3 loadperiod: 5 high: True suffix: True verbose: True veryverbose: True distribute: False cleanup: True getload: False translate: True useglobalconfig: True useglobalmap: True application name: l302.exel application lookup name: l302_exel local executable directory: /usr/local/g03/linda-exe distribution directory: /usr/local/g03/linda7.1/intel-linux2.4-rh8/ maxlicense: 1000000 ******************************************** ntsnet: trying to schedule 3 workers ntsnet: scheduled a total of 3 workers ******************************************** node name: xxx (...) node name.... (...) ntsnet: starting master process on at1 /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_sh /usr/local/g03/linda-exe/l302.exel 65536000 /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 +LARGS 5 0 -kainterval 1 -master 30997 -tsnetport 42530 -maxworkers 3 -minworkers 3 -minwait 600 -maxwait 600 -nodename at1 -kaon ntsnet: starting 1 worker on at1101.ime.eb.br /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh at1101.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 +LARGS 5 1 -maxworkers 3 -chdir /home/alex -worker at1:30997 -workerwait 900 -tsnetref 1 -nodename at1101xxx ntsnet: starting 1 worker on at1102.ime.eb.br /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh at1102.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 +LARGS 5 2 -maxworkers 3 -chdir /home/alex -worker at1:30997 -workerwait 900 -tsnetref 2 -nodename at1102xxx ntsnet: starting 1 worker on at1103.ime.eb.br /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh at1103.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 +LARGS 5 3 -maxworkers 3 -chdir /home/alex -worker at1:30997 -workerwait 900 -tsnetref 3 -nodename at1103xxx ntsnet: exec'ing /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/LindaLauncher /home/alex/tmp/viaExecDataaCXV13 $ After that, the job apparentelly freeze at link l302.exel. Nothing is running at nodes. $ps PID TTY TIME CMD 15837 pts0 00:00:00 bash 18731 pts0 00:00:00 g03l 18732 pts0 00:00:00 g03 18733 pts0 00:00:03 l302.exe 18735 pts0 00:00:00 cLindaLauncher 18738 pts0 00:00:01 l302.exel 18739 pts0 00:00:00 ssh 18740 pts0 00:00:00 ssh 18741 pts0 00:00:00 ssh 19034 pts0 00:00:00 ps To test the execution I have past the folowing command line (from ntsnet: starting 1 worker on at1101xxx) $/usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh at1101.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 +LARGS 5 1 -maxworkers 3 -chdir /home/alex -worker at1:30997 -workerwait 900 -tsnetref 1 -nodename at1101.ime.eb.br failed to look up given name -workerwait What can I change to work withou problems? Alexander. From owner-chemistry@ccl.net Thu Oct 20 12:46:01 2005 From: "Abrash, Samuel sabrash..richmond.edu" To: CCL Subject: CCL: A New Question on BSSE and ZPE corrections. Message-Id: <-29673-051020115353-32319-uF/iNo5GcWLCce+QB+dQNQ*_*server.ccl.net> X-Original-From: "Abrash, Samuel" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Thu, 20 Oct 2005 11:53:46 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash*richmond.edu] Hi All, In a recent paper on the structure of acetylene dimers, (J. Phys. Chem. A., Vol 103, No. 51, (1999), p 11431-11441), Alfred Karpfen says in his Method of Calculation Section, "The resulting stabilization energies were then corrected for zero point energy (ZPE) effects and for the basis set superposition error (BSSE) INCLUDING THE EFFECT OF GEOMETRY RELAXATION ON THE COMPLEXES. I have a few questions about this. First, what is geometry relaxation? Second, how can it be evaluated using G03? Third, Karpfen uses harmonic vibrational frequencies for his ZPE correction. How significant is the difference if one uses anharmonic vibrational frequencies for these weakly bound complexes, and given the status of the anharmonic calcultions in g03 is it worth the extra time. Thanks in advance to one and all for your responses. Best, Sam Abrash Department of Chemistry University of Richmond sabrash a richmond.edu From owner-chemistry@ccl.net Thu Oct 20 14:12:00 2005 From: "Sergio Emanuel Galembeck segalemb|,|usp.br" To: CCL Subject: CCL: A New Question on BSSE and ZPE corrections. Message-Id: <-29674-051020140737-32122-hfBV1KiH3E5K9OynkLbKbg(_)server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 20 Oct 2005 16:07:04 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb ~ usp.br] Dear Samuel, Geometry relaxation is the same as optimization of geometry. You can do this kind of calculation using the keywords counterpoise and opt. I am not sure about the third question. Best regards, Sergio PS: You can send an e-mail to Alfred Kapfren. He is a very nice person. Citando "Abrash, Samuel sabrash..richmond.edu" : > > Sent to CCL by: "Abrash, Samuel" [sabrash*richmond.edu] > Hi All, > > In a recent paper on the structure of acetylene dimers, (J. Phys. Chem. A., > Vol 103, No. 51, (1999), p 11431-11441), Alfred Karpfen says in his Method of > Calculation Section, "The resulting stabilization energies were then > corrected for zero point energy (ZPE) effects and for the basis set > superposition error (BSSE) INCLUDING THE EFFECT OF GEOMETRY RELAXATION ON THE > COMPLEXES. > > I have a few questions about this. > > First, what is geometry relaxation? > > Second, how can it be evaluated using G03? > > Third, Karpfen uses harmonic vibrational frequencies for his ZPE correction. > How significant is the difference if one uses anharmonic vibrational > frequencies for these weakly bound complexes, and given the status of the > anharmonic calcultions in g03 is it worth the extra time. > > Thanks in advance to one and all for your responses. > > Best, > Sam Abrash > Department of Chemistry > University of Richmond > sabrash---richmond.edu> > > > From owner-chemistry@ccl.net Thu Oct 20 16:10:00 2005 From: "Rzepa, Henry h.rzepa---imperial.ac.uk" To: CCL Subject: CCL: Stereo 3D Displays & Equipment Message-Id: <-29675-051020155235-26819-TT0KMLS66CFZDTzU0/He3Q---server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Thu, 20 Oct 2005 20:00:58 +0100 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa]![imperial.ac.uk] >Sent to CCL by: "Warren DeLano" [warren\a/delsci.com] > >Here is some current information for those of you ordering yourself a >new "Quad" Quadro-based Mac for doing Stereo 3D visualization. You will >need a good CRT display, a stereo signal emitter, and shutter glasses. > >Stereo 3D glasses & emitters: > >- More expensive: StereoGraphics >l> > >- Less expensive: NuVision3D > > >Thanks to LCD dominance, it is getting mucher harder to find a good CRT >display. You may need to hunt around a bit or buy "pre-owned". Can I add a counter argument FOR LCD rather than CRT displays. The programs listed at http://www.ddd.com/product/tridef/visualizer/enabled/ all use a LCD display made by Sharp to display 3D as "autostereo", ie without the need for head sets or special graphics. We have evaluated three of them, and find them pretty good (although not the very best I have ever seen), and particularly cost effective, given the more or less entry level cost of the system. An advantage is that on the smaller screen (15") perhaps 10 people can all view the display, and more on larger systems. Although I have not seen it myself, 43" displays can be procured (although these are getting expensive). -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs|-|mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Thu Oct 20 16:45:00 2005 From: "Godefroid Gahungu ggahungu%yahoo.fr" To: CCL Subject: CCL: W:Software Message-Id: <-29676-051020085157-698-IsfkCl91h8TfjxjPbVaTMg,;,server.ccl.net> X-Original-From: "Godefroid Gahungu" Sent to CCL by: "Godefroid Gahungu" [ggahungu]~[yahoo.fr] Hello! I am interested in the electronic structure investigation of a set molecules for which I would like to use the electron density, charge density and Laplacian plots/maps. Could someone tell what sofware/program to be used please? Thanks. From owner-chemistry@ccl.net Thu Oct 20 17:20:00 2005 From: "Arindam Ganguly arindamganguly^-^gmail.com" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29677-051020135843-17337-sXSWC3dbpvxYvVTv4UH7+A:_:server.ccl.net> X-Original-From: "Arindam Ganguly" Sent to CCL by: "Arindam Ganguly" [arindamganguly**gmail.com] Hi All, i am looking for a software whcih when given an input of the structure can tell us the Point Group to which the chemical belongs too. thanks. Arindam Ganguly UMKC(dept. of Chemistry) USA From owner-chemistry@ccl.net Thu Oct 20 17:55:00 2005 From: "karlo Mendoza Falla karlo_999]-[yahoo.es" To: CCL Subject: CCL: The x,y,z coordinat of porphyrins Message-Id: <-29678-051020115142-32143-s0jrMEsDJcN5WUWzoWsWzQ]^[server.ccl.net> X-Original-From: karlo Mendoza Falla Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 20 Oct 2005 17:51:25 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: karlo Mendoza Falla [karlo_999:+:yahoo.es] Usted puede dibujar la estructura con el modelador HYPERCHEM, hacer una optimización con el método semiempírico AM1, y luego hacer la matriz -Z para Gaussian 03. Espero haberlo ayudado . Bach. Qca.Karlo Edward Mendoza Falla. UNMSM-Lima. Perú. --- "may abdelghani may01dz**yahoo.fr" escribió: > > Sent to CCL by: may abdelghani [may01dz*yahoo.fr] > Dear CLLers, > > From were I Can, my CClers friend, find (or > obtain) > the (X, Y, Z) coordinate of anionic (H2TSPP and > NiTCPP) porphyrins > Thanks > > > > > > > > ___________________________________________________________________________ > > Appel audio GRATUIT partout dans le monde avec le > nouveau Yahoo! Messenger > Téléchargez cette version sur > http://fr.messenger.yahoo.com > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the ### > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST###ccl.net > or use> > Before posting check wait time for next message at: > http://www.ccl.net> > If your mail bounces from CCL with 5.7.1 error, > check:> > > > ______________________________________________ Renovamos el Correo Yahoo! Nuevos servicios, más seguridad http://correo.yahoo.es From owner-chemistry@ccl.net Thu Oct 20 18:29:01 2005 From: "Daniel Pechkis dlpech%a%wm.edu" To: CCL Subject: CCL: qz2p basis set for Gaussian Message-Id: <-29679-051020171645-26922-vDRx32rTofxfz+xZIS8+lQ||server.ccl.net> X-Original-From: Daniel Pechkis Content-Type: multipart/alternative; boundary="------------000201050706020004030204" Date: Thu, 20 Oct 2005 16:37:49 -0400 MIME-Version: 1.0 Sent to CCL by: Daniel Pechkis [dlpech(_)wm.edu] This is a multi-part message in MIME format. --------------000201050706020004030204 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit I'm new to Gaussian and I would like to reproduce the chemical shift calculations done in J. R. Cheeseman, G. W. Trucks, T. A. Keith, and M. J. Frisch, J. Chem. Phys 104 (14) 5497 (1996) with the qz2p (quadruple-zeta double polarization) basis set. My only problem is that I can't find the qz2p basis set. I was wondering if someone could give me some more information about how to use this basis set. Thanks, Dan Pechkis --------------000201050706020004030204 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit

I’m new to Gaussian and I would like to reproduce the chemical shift calculations done in

J. R. Cheeseman, G. W. Trucks, T. A. Keith, and M. J. Frisch, J. Chem. Phys 104 (14) 5497 (1996)

with the qz2p (quadruple-zeta double polarization) basis set. My only problem is that I can’t find the qz2p basis set. I was wondering if someone could give me some more information about how to use this basis set.

Thanks,

Dan Pechkis

--------------000201050706020004030204-- From owner-chemistry@ccl.net Thu Oct 20 19:04:00 2005 From: "Joe Golab joseph.golab!A!innovene.com" To: CCL Subject: CCL: W:ANNOUNCEMENT: FOMMS 2006 Registration is OPEN Message-Id: <-29680-051020170712-25986-hJWtq0yvCp4QByRJ5hAPAQ%%server.ccl.net> X-Original-From: "Joe Golab" Sent to CCL by: "Joe Golab" [joseph.golab**innovene.com] Dear Colleague: We are pleased to send you this announcement for the 3rd Foundations of Molecular Modeling and Simulation (FOMMS 2006) conference to be held July 9th - 14th 2006 at Semiahmoo Resort (www.semiahmoo.com), in Blaine, WA, USA. Like its predecessors, FOMMS 2006 will be a scientific meeting balanced between the methods of quantum mechanics, atomistic simulation, mesoscale methods and beyond, and application areas in chemistry, biology, materials and their respective industries. FOMMS is the only focused conference that brings together the modeling community and emphasizes integration from the most fundamental level (electronic structure) through atomistic to meso- and macro-scale modeling. For additional information about the conference please visit our web site at http://www.fomms.org, or contact us directly at chair!^!fomms.org. We look forward to your participation in the conference. Joe Golab and Clare McCabe Chairs, FOMMS 2006 From owner-chemistry@ccl.net Thu Oct 20 20:11:00 2005 From: "Serguei Patchkovskii ps||ned.sims.nrc.ca" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29681-051020194106-14812-dSTmc4k7q7/tZkHuJp78Ew^-^server.ccl.net> X-Original-From: Serguei Patchkovskii Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 20 Oct 2005 18:45:59 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Serguei Patchkovskii [ps#,#ned.sims.nrc.ca] On Thu, 20 Oct 2005, Arindam Ganguly arindamganguly^-^gmail.com wrote: > i am looking for a software whcih when given an input of the structure can > tell us the Point Group to which the chemical belongs too. thanks. http://www.cobalt.chem.ucalgary.ca/ps/symmetry/ The nice feature of this one is that it can also find approximate symmetries, and tell you how far your structure is from having the exact symmetry elements. Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii===nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From owner-chemistry@ccl.net Thu Oct 20 21:54:00 2005 From: "T. Daniel Crawford crawdad---exchange.vt.edu" To: CCL Subject: CCL: qz2p basis set for Gaussian Message-Id: <-29682-051020213736-17438-gcyV/Xg44Ov+6rHjuKPyRA[*]server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-type: multipart/alternative; boundary="B_3212686220_72222" Date: Thu, 20 Oct 2005 20:50:20 -0400 Mime-version: 1.0 Sent to CCL by: "T. Daniel Crawford" [crawdad()exchange.vt.edu] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3212686220_72222 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Dan, The original basis set doesn=B9t seem to be available as stated in the original paper by Ahlrichs and co-workers. However, the AcesII code does include this basis =8B at least, the contraction matches that described in both the Cheeseman article and the Gauss article it cites, and the referenc= e is correct: http://tcwork08.chemie.uni-mainz.de/download/GENBAS Search for =B3qz2p=B2 on this file and you=B9ll find the basis for H, B, C, N, O, F, P, and Cl. -Daniel=20 On 10/20/05 4:37 PM, "Daniel Pechkis dlpech%a%wm.edu" wrote: > I=B9m new to Gaussian and I would like to reproduce the chemical shift > calculations done in >=20 > J. R. Cheeseman, G. W. Trucks, T. A. Keith, and M. J. Frisch, J. Chem. P= hys > 104 (14) 5497 (1996) >=20 > with the qz2p (quadruple-zeta double polarization) basis set. My only pro= blem > is that I can=B9t find the qz2p basis set. I was wondering if someone could= give > me some more information about how to use this basis set. >=20 > Thanks, >=20 > Dan Pechkis >=20 --=20 T. Daniel Crawford Department of Chemistry crawdad!A!vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-325= 5 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt --B_3212686220_72222 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Re: CCL: qz2p basis set for Gaussian Dan,<= BR>
The original basis set doesn’t seem to be available as stated in the = original paper by Ahlrichs and co-workers.  However, the AcesII code do= es include this basis — at least, the contraction matches that describ= ed in both the Cheeseman article and the Gauss article it cites, and the ref= erence is correct:

http://tcwork= 08.chemie.uni-mainz.de/download/GENBAS

Search for “qz2p” on this file and you’ll find the basis = for H, B, C, N, O, F,  P, and Cl.

-Daniel


On 10/20/05 4:37 PM, "Daniel Pechkis dlpech%a%wm.edu" <owner-c= hemistry!A!ccl.net> wrote:

I’m new to Gaussian and I would like to reproduce= the chemical shift calculations done in

 J. R. Cheeseman, G. W. Trucks, T. A. Keith, and M. J. Frisch, J. Chem= . Phys 104 (14) 5497 (1996)

with the qz2p (quadruple-zeta double polarization) basis set. My only probl= em is that I can’t find the qz2p basis set. I was wondering if someone= could give me some more information about how to use this basis set.

Thanks,

Dan Pechkis



--
T. Daniel Crawford          &n= bsp;            =     Department of Chemistry
crawdad!A!vt.edu           =             &nbs= p;            Vi= rginia Tech
www.chem.vt.edu/faculty/crawford.php  Voice: 540-231-7760  FAX: 5= 40-231-3255
            &nb= sp;            &= nbsp;  --------------------
 PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt<= BR> --B_3212686220_72222-- From owner-chemistry@ccl.net Thu Oct 20 23:20:00 2005 From: "Dmitri Goussev dgoussev:+:wlu.ca" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29683-051020225110-20684-lzOJtoF4iRhZqf0/fNliOA . server.ccl.net> X-Original-From: "Dmitri Goussev" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0026_01C5D5C2.2F6A1420" Date: Thu, 20 Oct 2005 22:04:04 -0400 MIME-Version: 1.0 Sent to CCL by: "Dmitri Goussev" [dgoussev:-:wlu.ca] This is a multi-part message in MIME format. ------=_NextPart_000_0026_01C5D5C2.2F6A1420 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Serguei, I am not sure whether this page is available from non-UofC = computers. Dmitri=20 ----- Original Message -----=20 From: Serguei Patchkovskii ps||ned.sims.nrc.ca=20 To: Goussev, Dmitri =20 Sent: Thursday, October 20, 2005 6:45 PM Subject: CCL: W:Calculation of Point Group Sent to CCL by: Serguei Patchkovskii [ps#,#ned.sims.nrc.ca] On Thu, 20 Oct 2005, Arindam Ganguly arindamganguly^-^gmail.com wrote: > i am looking for a software whcih when given an input of the = structure can=20 > tell us the Point Group to which the chemical belongs too. thanks. http://www.cobalt.chem.ucalgary.ca/ps/symmetry/ The nice feature of this one is that it can also find approximate=20 symmetries, and tell you how far your structure is from having the exact symmetry elements. Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii * nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada -=3D This is automatically added to each message by the mailing script = =3D- To recover the email address of the author of the message, please = changehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job advertisements: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt =------=_NextPart_000_0026_01C5D5C2.2F6A1420 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Serguei, I am not sure whether this = page is=20 available from non-UofC computers.
Dmitri 
----- Original Message -----
From:=20 Serguei=20 Patchkovskii ps||ned.sims.nrc.ca
Sent: Thursday, October 20, = 2005 6:45=20 PM
Subject: CCL: W:Calculation of = Point=20 Group


Sent to CCL by: Serguei Patchkovskii=20 [ps#,#ned.sims.nrc.ca]
On Thu, 20 Oct 2005, Arindam Ganguly=20 arindamganguly^-^gmail.com wrote:

> i am looking for a = software=20 whcih when given an input of the structure can
> tell  us = the=20 Point Group to which the chemical belongs too. thanks.

http://www.cobal= t.chem.ucalgary.ca/ps/symmetry/

The=20 nice feature of this one is that it can also find approximate =
symmetries,=20 and tell you how far your structure is from having the
exact = symmetry=20 elements.

Serguei

---
Dr. Serguei = Patchkovskii

Tel:=20 +1-(613)-990-0945
Fax: +1-(613)-947-2838
E-mail: = Serguei.Patchkovskii *=20 nrc.ca

Coordinator of Modelling Software
Theory and = Computation=20 Group
Steacie Institute for Molecular Sciences
National Research = Council=20 Canada
Room 2011, 100 Sussex Drive
Ottawa, Ontario
K1A 0R6=20 Canada



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To recover the email address of the author of = the=20 message, please change
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