From owner-chemistry@ccl.net Wed Jan 23 04:51:00 2008 From: "Sina T reli sinatureli[#]gmail.com" To: CCL Subject: CCL: Computational Spectroscopy Message-Id: <-36091-080123044906-4739-xjzmDL7/S1jO0TH0++ZsCA::server.ccl.net> X-Original-From: "Sina T reli" Date: Wed, 23 Jan 2008 04:49:02 -0500 Sent to CCL by: "Sina T reli" [sinatureli ~ gmail.com] Hello, I have some questions regarding computational spectroscopy. My aim is to find the spectral orbital overlap between some molecules (namely chlorophylls). I use arguslab to produce the transition wavelengths and use a homogenous linewidth of 2nm to produce graphs of absorption with width. However I need a method for determining also their emission spectra and for that since they are quite immobile in their enviroment a mirror image about the 0->0 transition is suggested in some literatures and books. My question is is there a way in which I can find where in the graph is this 0->0 transition is supposed to be. I know it is near the end but since I am going to calculate spectral overlap of molecules, I need a more precise way of finding it.. Or is there any tool that will produce the emission spectra of molecules? Second question comes to users of arguslab. When a spectral analysis is done on the molecule at any given transition dipole electric length and state dipole length. Are these measured in debye or do they just give the directions of the dipoles. If I am looking for the magnitute of transition dipole moment of any given transition, is the length of this transition dipole electric length that will give me the value? Thanks in advance for your answers. From owner-chemistry@ccl.net Wed Jan 23 06:51:00 2008 From: "Jens Spanget-Larsen spanget#ruc.dk" To: CCL Subject: CCL:G: Potential Surface Scan Message-Id: <-36092-080123045829-8554-dttFXCZCQ7JFRv3q5So+OA[a]server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Jan 2008 10:00:25 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget*_*ruc.dk] Dear Jitrayut, this happens all the time! If you are unlucky, and you cannot extract the energies from the archive file (as suggested by William), you can find the energies by searching the output file for "stationary points", see below. Yours, Jens >--< - - - SCF Done: E(RB+HF-LYP) = -1026.57682940 A.U. after 12 cycles Convg = 0.2554D-08 -V/T = 2.0046 S**2 = 0.0000 - - - Item Value Threshold Converged? Maximum Force 0.000180 0.002500 YES RMS Force 0.000060 0.001667 YES Maximum Displacement 0.007506 0.010000 YES RMS Displacement 0.002383 0.006667 YES Optimization completed. -- Stationary point found. ---------------------------- ! Optimized Parameters ! ! (Angstroms and Degrees) ! -------------------------- -------------------------- ! Name Definition Value Derivative Info. ! -------------------------------------------------------------------------------- ! R1 R(1,2) 2.1764 -DE/DX = 0.0 ! ! R2 R(1,3) 1.4668 -DE/DX = 0.0001 ! ! R3 R(1,4) 1.4652 -DE/DX = 0.0001 ! ! R4 R(1,6) 1.8121 -DE/DX = 0.0001 ! ! R5 R(2,5) 1.8318 -DE/DX = 0.0 ! ! R6 R(5,7) 1.0942 -DE/DX = 0.0 ! ! R7 R(5,8) 1.0916 -DE/DX = 0.0 ! - - - ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget[]ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ William F. Polik polik]=[hope.edu wrote: > > Sent to CCL by: "William F. Polik" [polik__hope.edu] > Jitrayut, > > We have seen this before with Gaussian. I suspect that your molecule > is large enough that its computed energy is less than -1000 au. The > formatting statement used to output this line is evidently limited to > -999.99999, and consequently "**********" is output instead. > > If your are lucky, you might be able to extract the numbers from the > archive section of the output (at the very end). > > Will Polik > > At 12:53 AM 1/22/2008, you wrote: >> Dear CCL community, >> >> I have problem about the output of running Potential Surface Scan in >> line " Summary of Optimized Potential Surface Scan"with the following >> input; >> >> %chk=test-BF.chk >> %mem=6MW >> %nproc=1 >> # hf/6-31g opt=z-matrix nosymm >> >> C 21 B22 2 A21 1 >> tor >> tor 0.0 S 13 +15.0 >> >> The output error is the Eigenvalue which is ****** what is this >> symbol? when i try with AM1 calculation the Eigenvalue is ok. So, is >> there something mistage about the method or just my mistage somewhere >> please check the output below. >> >> Summary of Optimized Potential Surface Scan >> 1 2 3 4 5 >> EIGENVALUES -- ************************************************** >> B1 1.39996 1.39889 1.39745 1.39626 1.39516 >> B2 1.40273 1.40203 1.40051 1.39910 1.39808 >> B3 1.37890 1.37911 1.37962 1.38022 1.38077 >> B4 1.39459 1.39530 1.39610 1.39654 1.39669 >> B5 1.38309 1.38363 1.38428 1.38464 1.38467 >> B6 1.06927 1.07052 1.07196 1.07284 1.07317 >> B7 1.07010 1.07150 1.07294 1.07369 1.07397 >> D17 -179.99458-180.01870-180.00589-179.99765-179.98866 >> D18 -180.00074-177.98783-178.74325-180.06775-180.97743 >> D19 - 179.99528-161.51052-147.91222-135.19630-121.68689 >> tor 0.00000 15.00000 30.00000 45.00000 60.00000 >> Anyone who have experienced in this problem, please help me !! >> >> Best regards, >> >> Jitrayut Jitonnom >> >> > > ================================ > Dr. William F. Polik > Hofma Professor of Chemistry > > Department of Chemistry > Hope College > 35 East 12th Street > Holland, MI 49422-9000 > USA > > polik]|[hope.edu > http://www.chem.hope.edu/~polik > tel: (616) 395-7639 > fax: (616) 395-7118 > ================================http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Jan 23 08:53:01 2008 From: "qing ni mr.alchem_-_gmail.com" To: CCL Subject: CCL:G: Problem with scanning through bond dissociation Message-Id: <-36093-080123032133-16920-SgOtoplVBBcb3k/rwMjEJg . server.ccl.net> X-Original-From: "qing ni" Date: Wed, 23 Jan 2008 03:21:30 -0500 Sent to CCL by: "qing ni" [mr.alchem(~)gmail.com] When I used Gaussian03 to scan the potential energy of CF2=CF2, where C=C bond elongates until the molecules separates to two CF2, what I see is that the energy curve shows an abrupt drop somewhere. This is strange because I expect the curve to be a smooth hill-like profile, instead of a broken line. When I use smaller step size to scan the profile just near the broken edge, I found a smooth droping line, with some of the single point energy being different from that was calculated previously. What is the problem? Is there any way to cope with this situation? From owner-chemistry@ccl.net Wed Jan 23 09:28:00 2008 From: "Jose Ceron jpceron#,#um.es" To: CCL Subject: CCL: Problems with Gaussian03 SCRF optimization Message-Id: <-36094-080123044240-3930-qjY9DWTj4Oo28uXrBihlZg*server.ccl.net> X-Original-From: "Jose Ceron" Date: Wed, 23 Jan 2008 04:42:36 -0500 Sent to CCL by: "Jose Ceron" [jpceron:+:um.es] Hello everybody, I'm trying to carry out the optimization of a DNA basis pair in a high dielectric constant medium (120), so I have to use the dielectric=120.0 option with SCRF keyword. I think methods like PCM, IEFPCM ... are not available for OPT when you edit the dielectric constant, so it is necessary to use scipcm. But I obtain next error: Surface Problems in SciFoc When I use SCF with direct and/or SCRF with gascavity options the error is: >>>>>>>>>> Convergence criterion not met. Convergence failure -- run terminated. Any suggestion? Thanks very much in advanced. Jose P. Ceron University of Murcia From owner-chemistry@ccl.net Wed Jan 23 10:05:00 2008 From: "jeff mathieu gregory licpro.dechets++gmail.com" To: CCL Subject: CCL:G: g03 and openmpi Message-Id: <-36095-080123035345-19627-x3mP5+jP8Fd5l0jGtHKbAA . server.ccl.net> X-Original-From: "jeff mathieu gregory" Date: Wed, 23 Jan 2008 03:53:40 -0500 Sent to CCL by: "jeff mathieu gregory" [licpro.dechets^gmail.com] Hello CCLers, Is it possible to compile Gaussian03 with Openmpi? My problem is that Linda cause me trouble with torque (PBS) queueing system. Thank you for your help, Jeff From owner-chemistry@ccl.net Wed Jan 23 10:39:01 2008 From: "gestionnaire licpro licpro.dechets:gmail.com" To: CCL Subject: CCL:G: g03 and openmpi Message-Id: <-36096-080122134533-31104-PQpIwvNQopYT19nGeOWqnQ]![server.ccl.net> X-Original-From: "gestionnaire licpro" Content-Type: multipart/alternative; boundary="----=_Part_15732_29618700.1201020550405" Date: Tue, 22 Jan 2008 17:49:10 +0100 MIME-Version: 1.0 Sent to CCL by: "gestionnaire licpro" [licpro.dechets*gmail.com] ------=_Part_15732_29618700.1201020550405 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello CCLers, Is it possible to compile Gaussian03 with Openmpi? My problem is that Linda cause me trouble with torque (PBS) queueing system. Thank you for your help, Jeff ------=_Part_15732_29618700.1201020550405 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello CCLers,

Is it possible to compile Gaussian03 with Openmpi?
My problem is that Linda cause me trouble with torque (PBS) queueing system.

Thank you for your help,
Jeff
------=_Part_15732_29618700.1201020550405-- From owner-chemistry@ccl.net Wed Jan 23 11:13:00 2008 From: "Shrin Pal spalindia,+,gmail.com" To: CCL Subject: CCL: charge transfer Message-Id: <-36097-080123014350-5716-3RpsV2yi+fftzOctASjPbg]_[server.ccl.net> X-Original-From: "Shrin Pal" Content-Type: multipart/alternative; boundary="----=_Part_424_21112541.1201067160297" Date: Wed, 23 Jan 2008 11:16:00 +0530 MIME-Version: 1.0 Sent to CCL by: "Shrin Pal" [spalindia() gmail.com] ------=_Part_424_21112541.1201067160297 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All, I require some urgent help from you people: Is there a charge transfer / energy transfer mechanism in which the Energy of the systems is proportional to 1/r where r is the distance of separation between the donor and acceptor? Any references would be really really helpful. -- Thanks Shrinwantu Pal Prof. Pati's Lab TSU JNCASR Jakkur Bangalore 560064 India www.jncasr.ac.in/pati ------=_Part_424_21112541.1201067160297 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All,

I require some urgent help from you people:

Is there a charge transfer / energy transfer mechanism in which the Energy of the systems is proportional to 1/r
where r is the distance of separation between the donor and acceptor?

Any references would be really really helpful.

-- Thanks

Shrinwantu Pal

Prof. Pati's Lab
TSU
JNCASR
Jakkur
Bangalore 560064
India
www.jncasr.ac.in/pati ------=_Part_424_21112541.1201067160297-- From owner-chemistry@ccl.net Wed Jan 23 11:50:00 2008 From: "Pierre Archirel pierre.archirel[A]lcp.u-psud.fr" To: CCL Subject: CCL: SCRF optimisation Message-Id: <-36098-080123104245-31579-tzrnmJSEzRnRMJhx/8BwIA**server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Jan 2008 16:56:50 +0100 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel[a]lcp.u-psud.fr] This is an answer to J. Ceron: It should be possible to optimise geometries with PCM and a modified dielectric constant, but you must define all the parameters: #.... scrf=(pcm,read) opt ... pcmdoc eps=120. rsolv=xxx vmol=xxx (cm3!) density=xxx dereps=xxx ... the parameters are defined in utilam.F and utilnz.F Hopes this helps __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel%a%lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Wed Jan 23 12:23:00 2008 From: "Justin Finnerty justin.finnerty],[uni-oldenburg.de" To: CCL Subject: CCL:G: g03 and openmpi Message-Id: <-36099-080123114112-13000-tNhtP8lFy+gZ2nGWmXSn7g,+,server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 23 Jan 2008 17:40:47 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty%a%uni-oldenburg.de] On Wed, 2008-01-23 at 03:53 -0500, jeff mathieu gregory licpro.dechets ++gmail.com wrote: > Sent to CCL by: "jeff mathieu gregory" [licpro.dechets^gmail.com] > Hello CCLers, > > Is it possible to compile Gaussian03 with Openmpi? > My problem is that Linda cause me trouble with torque (PBS) queueing system. I think the answer to this is definitely no. What is the problem with torque? I use torque and have no problem running Linda jobs. The only reason I can think of is if your sysadmin team is insisting that you use the resource manager for job transfer and has disabled rsh. If that is the case then suggest that they either: 1) configure Linda/ntsnet to use ssh (if ssh is not also disabled). 2) use torque PAM authentication modules for limiting remote logins instead of completely disabling rsh/ssh. 3) set up Linda/ntsnet to use pbsdsh. If your sysadmin does get option 3 working please let me know as I tried and failed... Cheers Justin -- Dr Justin Finnerty Rm W3-1-218 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Jan 23 12:58:00 2008 From: "Gerhard Wolber wolber##inteligand.com" To: CCL Subject: CCL: LigandScout 2.0 released Message-Id: <-36100-080123123750-25291-QFVkWDEHn2hdPvFzobcALA(!)server.ccl.net> X-Original-From: "Gerhard Wolber" Date: Wed, 23 Jan 2008 12:37:46 -0500 Sent to CCL by: "Gerhard Wolber" [wolber-,-inteligand.com] Dear colleagues, we would like to announce the new version 2.0 of our 3D pharmacophore modeling application LigandScout. LigandScout allows for sophisticated 3D pharmacophore generation from macromolecule-ligand complexes, pharmacophore overlay and interpolation, a lightning fast and robust pharmacophore-based alignment algorithm that allows creating consensus pharmacophores and merged feature pharmacophores. In version 2.0 we added support for various new file formats, including pharmacophore export to Catalyst(tm), Phase(tm), and MOE(tm), metal complexing features for Iron, Magnesium and Zinc, as well as spreadsheet functionality that allows for re-scoring of docking results according to pharmacophores or refitting screening results from other programs. Additionally, there is a full-featured implementation of MMFF94s that allows for approximated calculation of strain energies, molecule modification with on-the-fly minimization, and minimization of screening results in the binding site. More information along with an on-line manual can be found on our website (http://www.inteligand.com/ligandscout), as well as a fully functional evaluation version for download (http://www.inteligand.com/ligandscout/download.shtml). The software is very affordable for academic institutions, and we also offer software grants. We appreciate any feed-back including feature requests and comments. Best regards, Gerhard Wolber -- Dr. Gerhard Wolber Executive Partner, Head of Technology Inte:Ligand Software-Entwicklungs- und Consulting GmbH Mariahilferstrasse 74B/11 1070 Wien/Vienna Phone +43 699 15075000 Fax +43 1 8174955 1371 Web: www.inteligand.com Mail: wolber _ inteligand.com From owner-chemistry@ccl.net Wed Jan 23 15:28:00 2008 From: "David Gallagher gallagher.da[A]gmail.com" To: CCL Subject: CCL: Teaching thermodynamics Message-Id: <-36101-080123145028-12347-qAqr/j2YqMV0PfJ8v0t9Ng!=!server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_14259281==.ALT" Date: Wed, 23 Jan 2008 10:34:33 -0800 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da===gmail.com] --=====================_14259281==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed New SW tool for teaching fluid-phase thermodynamics: A special teaching version of the award-winning COSMOtherm package is now available. COSMOtherm predicts a wide range of properties for mixtures and pure compounds, such as partition coefficients, phase equilibria, azeotropes, activity coefficients, vapor pressures, solubilities, sigma profiles, and much more. COSMOtherm-Edu includes a permanent license for one professor with a limited database of about 280 common compounds and solvents (including ionic liquids), along with an annual class license so that students can run experiments with COSMOtherm-Edu on their own laptops. For pricing and more info visit http://www.cacheresearch.com/cosmo.html David Gallagher CAChe Research --=====================_14259281==.ALT Content-Type: text/html; charset="us-ascii" New SW tool for teaching fluid-phase thermodynamics:

A special teaching version of the award-winning COSMOtherm package is now available.  COSMOtherm predicts a wide range of properties for mixtures and pure compounds, such as partition coefficients, phase equilibria, azeotropes, activity coefficients, vapor pressures, solubilities, sigma profiles, and much more.

COSMOtherm-Edu includes a permanent license for one professor with a limited database of about 280 common compounds and solvents (including ionic liquids), along with an annual class license so that students can run experiments with COSMOtherm-Edu on their own laptops.

For pricing and more info visit http://www.cacheresearch.com/cosmo.html

David Gallagher
CAChe Research --=====================_14259281==.ALT-- From owner-chemistry@ccl.net Wed Jan 23 21:11:01 2008 From: "enb_-_rice.edu" To: CCL Subject: CCL: Upper limit of CCSD(T) Message-Id: <-36102-080123203422-29953-FJWn9HttILgkWwuv9rFtXg^^server.ccl.net> X-Original-From: enb=-=rice.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 23 Jan 2008 18:28:00 -0600 MIME-Version: 1.0 Sent to CCL by: enb*o*rice.edu Is anyone aware of the upper limit in terms of systems size for CCSD(T) at the current level of computer technology? In other words, what is the biggest system investigated with a reasonable basis set and CCSD(T) that has been published? I spent a bit of time trying to track this down in the literature, and then realized that whoever wrote the paper probably also reads CCL. Thanks for your responses, Ed Brothers. From owner-chemistry@ccl.net Wed Jan 23 23:48:00 2008 From: "Jeff Hammond jeff.science*_*gmail.com" To: CCL Subject: CCL: Upper limit of CCSD(T) Message-Id: <-36103-080123234536-13305-amBZuDHNuvcRrpdRNoUf0Q:server.ccl.net> X-Original-From: "Jeff Hammond" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 23 Jan 2008 22:45:23 -0600 MIME-Version: 1.0 Sent to CCL by: "Jeff Hammond" [jeff.science||gmail.com] Ed, I'm fairly certain this is the largest CCSD(T) calculation ever performed... J. Phys. Chem. A, 109 (31), 6934 -6938, 2005 - http://pubs.acs.org/cgi-bin/abstract.cgi/jpcafh/2005/109/i31/abs/jp044564r.html Relevant excerpt: ============================================================== All of the calculations were performed with the NWChem suite of programs and Ecce (Extensible Computational Chemistry Environment), a problem-solving environment. The calculations were done on a massively parallel HP Linux cluster with Itanium-2 processors. The largest calculation performed was the CCSD(T) calculation on octane with 1468 basis functions (the aug-cc-pVQZ basis set). The perturbative triples (T) for octane took 23 h on 1400 processors, yielding 75% CPU efficiency and a sustained performance of 6.3 TFlops. Fourteen iterations were required for convergence of the CCSD, which took approximately 43 h on 600 processors. ============================================================== I should note that this is the old CCSD(T) code in NWChem, which does not fully exploit molecular symmetry. I don't know what the latest and greatest result for the TCE-based (spin-orbital, full use of symmetry) CCSD(T) code are, but Bert (http://emslbios.pnl.gov/id/dejong_wa) should be able to tell you. Recent work using other programs which may be relevant to your quest includes: Aces - J. Chem. Theory Comput., 4 (1), 64 -74, 2008 - http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2008/4/i01/abs/ct700152c.html GAMESS - J. Chem. Theory Comput., 3 (4), 1312 -1328, 2007 - http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2007/3/i04/abs/ct600366k.html PQS - J. Chem. Theory Comput., 3 (4), 1368 -1377, 2007 - http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2007/3/i04/abs/ct700048u.html Best, Jeff On Jan 23, 2008 6:28 PM, wrote: > > Sent to CCL by: enb*o*rice.edu > Is anyone aware of the upper limit in terms of systems size for CCSD(T) at the > current level of computer technology? In other words, what is the biggest > system investigated with a reasonable basis set and CCSD(T) that has been > published? I spent a bit of time trying to track this down in the literature, > and then realized that whoever wrote the paper probably also reads CCL. > > Thanks for your responses, > Ed Brothers.