From chemistry-request@ccl.net Mon Apr 4 22:53:22 2005 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j352rGOh005069 for < ccl.net>; Mon, 4 Apr 2005 22:53:16 -0400 Received: from hymn10.u.washington.edu (hymn10.u.washington.edu [140.142.13.244]) by mxout4.cac.washington.edu (8.13.3+UW05.01/8.13.3+UW05.01) with ESMTP id j351goer030798 for < ccl.net>; Mon, 4 Apr 2005 18:42:50 -0700 Received: from localhost (localhost [127.0.0.1]) by hymn10.u.washington.edu (8.13.3+UW05.01/8.13.3+UW05.01) with ESMTP id j351gnPx023052 for < ccl.net>; Mon, 4 Apr 2005 18:42:50 -0700 Received: from [140.142.12.169] by hymn10.u.washington.edu via HTTP; Mon, 04 Apr 2005 18:42:49 PDT Date: Mon, 4 Apr 2005 18:42:49 -0700 (PDT) From: liaoyi >< u.washington.edu To: chemistry >< ccl.net Subject: how fast a molecule absorbs a photon Message-ID: < hymn10.u.washington.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=1.3 required=5.0 tests=BLANK_LINES_70_80, NO_REAL_NAME autolearn=no version=3.0.1 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi, I have a very basic question for your opinion. When a molecule absorbs a photon, it will be excited to a excited state that has the same atomic geometry but different electron density distribution. I wonder how fast this process is? i.e. how fast the electron density distribution change from the ground state to excited state? Yi From chemistry-request@ccl.net Tue Apr 5 01:05:39 2005 Received: from SXT-SM-1.UCIS.Dal.Ca (SXT-SM-1.UCIS.Dal.Ca [129.173.5.72]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3555YML008624 for ; Tue, 5 Apr 2005 01:05:35 -0400 Received: from KIL-UPT-3.UCIS.Dal.Ca (KIL-UPT-3.UCIS.Dal.Ca [129.173.1.118]) by SXT-SM-1.UCIS.Dal.Ca (8.12.11/8.12.11) with ESMTP id j3555YeO015239; Tue, 5 Apr 2005 02:05:34 -0300 Received: from KIL-UPT-3.UCIS.Dal.Ca (localhost.localdomain [127.0.0.1]) by KIL-UPT-3.UCIS.Dal.Ca (8.12.11/8.12.11) with ESMTP id j3555Xmj007367; Tue, 5 Apr 2005 02:05:33 -0300 Received: (from apache@localhost) by KIL-UPT-3.UCIS.Dal.Ca (8.12.11/8.12.11/Submit) id j3555XwC007364; Tue, 5 Apr 2005 02:05:33 -0300 Received: from blk-224-150-196.eastlink.ca (blk-224-150-196.eastlink.ca [24.224.150.196]) by my3.dal.ca (IMP) with HTTP for ; Tue, 5 Apr 2005 02:05:33 -0300 Message-ID: <1112677533.42521c9d1d24c!at!my3.dal.ca> Date: Tue, 5 Apr 2005 02:05:33 -0300 From: Cherif Matta To: chemistry!at!ccl.net Cc: help!at!gaussian.com, Russell Boyd , Norberto Castillo Subject: CCL: Gaussian03 Disk Space Error in MP2 References: <57ffe604158f.425007dd!at!jhumail.jhu.edu> In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.4 X-Originating-IP: 24.224.150.196 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear all, We are trying to perform a single point calculation on a fairly large system using G03. We have a disk-space error in spite of the availability of much more free disk space than required in the error message. This is a neutral closed-shell system with 1014 basis functions, 1548 primitive gaussians, and 272 electrons. We are running it on a 64-bit SuSe9.1 Linux Box with 100 GB empty disk space. Since this is not a 32-bits system, the file size should not be a problem. The following is the Gaussian03 input line: ============================================ #p MP2(full, verystingy)/6-311++g** output=wfn density=current MaxDisk=65GB scf=(MaxCycle=200, tight) 6d 10f After the convergence of the SCF, the job is aborted, and the following is the error we get: ================================== Cycle 2 Pass 1 IDiag 1: RMSU= 4.56D-08 CP: 1.00D+00 E= -1864.55241471435 Delta-E= -0.000000000020 Rises=F Damp=F DIIS: error= 1.72D-09 at cycle 2 NSaved= 2. NSaved= 2 IEnMin= 2 EnMin= -1864.55241471435 IErMin= 2 ErrMin= 1.72D-09 ErrMax= 1.72D-09 EMaxC= 1.00D-01 BMatC= 9.11D-16 BMatP= 1.96D-14 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: 0.195D-01 0.980D+00 Coeff: 0.195D-01 0.980D+00 Gap= 0.295 Goal= None Shift= 0.000 RMSDP=6.47D-09 MaxDP=6.88D-07 DE=-2.00D-11 OVMax= 5.82D-09 SCF Done: E(RHF) = -1864.55241471 A.U. after 2 cycles Convg = 0.6466D-08 -V/T = 2.0011 S**2 = 0.0000 KE= 1.862590819875D+03 PE=-1.379542208284D+04 EE= 5.357304786856D+03 Leave Link 502 at Sat Apr 2 04:00:29 2005, MaxMem= 31457280 cpu: 11736.6 (Enter /home/programs/g03/l801.exe) Range of M.O.s used for correlation: 1 1009 NBasis= 1014 NAE= 136 NBE= 136 NFC= 0 NFV= 0 NROrb= 1009 NOA= 136 NOB= 136 NVA= 873 NVB= 873 **** Warning!!: The largest alpha MO coefficient is 0.13325828D+03 Leave Link 801 at Sat Apr 2 04:00:29 2005, MaxMem= 31457280 cpu: 0.1 (Enter /home/programs/g03/l906.exe) Not enough disk for semidirect, minimum= 946930225 Not enough memory for fully direct, minimum= 141181640. Not enough resources for E2 calculation. Error termination via Lnk1e in /home/programs/g03/l906.exe at Sat Apr 2 04:00:30 2005. ======================================================== We tried to run the job on a cluster with RedHat Linux where the scratch files were broken, each into 6 x 2GB-files, but we got exactly the same error message despite the availability of a huge disk space. Can someone help with this? I will summarize. Thank you very much in advance. Cheers, Cherif ------------------------------------------------------- Cherif F. Matta, Ph.D., MCIC * Izaak Walton Killam Post Doctoral Fellow Department of Chemistry, Dalhousie University Halifax, NS, Canada. * Adjunct Professor of Chemistry McMaster University, Hamilton, ON, Canada. ------------------------------------------------------- * Web site: http://chem.utoronto.ca/~cmatta/ Tel: (902) 494 7021 Fax: (902) 494 1310 ------------------------------------------------------- From chemistry-request@ccl.net Tue Apr 5 05:15:59 2005 Received: from theory.phys.ucl.ac.uk (gallifrey.phys.ucl.ac.uk [128.40.5.210]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j359FpGo023666 for ccl.net>; Tue, 5 Apr 2005 05:15:52 -0400 Received: from order (order.phys.ucl.ac.uk [128.40.5.31]) by theory.phys.ucl.ac.uk (8.12.9/8.12.8) with ESMTP id j3588jNH098537 for ccl.net>; Tue, 5 Apr 2005 09:08:46 +0100 (BST) (envelope-from j.tennyson <> ucl.ac.uk) Date: Tue, 5 Apr 2005 09:01:35 +0100 (BST) From: Jonathan Tennyson ucl.ac.uk> X-X-Sender: jonny <> order.phys.ucl.ac.uk To: chemistry <> ccl.net Subject: QuantemolN Message-ID: order.phys.ucl.ac.uk> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net 5 April 2005 Today we have launched the QuantemolN software package: an expert system for performing ab initio electron molecule collision calculation using the UK Molecular R-matrix code. For further information see: www.quantemol.com -- Jonathan Tennyson, Department of Physics & Astronomy, mailto: j.tennyson <> ucl.ac.uk University College London, Tel (work): +(44) 20 7679 7155 Gower Street, Tel (home): +(44) 20 8340 9225 London WC1E 6BT, UK Fax (if you must): +(44) 20 7679 7145 http://www.tampa.phys.ucl.ac.uk/jonny From chemistry-request@ccl.net Tue Apr 5 06:48:22 2005 Received: from mrbusi1.netcologne.de (mrbusi1.netcologne.de [194.8.194.213]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j35AmE7K028757 for ccl.net>; Tue, 5 Apr 2005 06:48:15 -0400 Received: from cosmologic.de (xdsl-213-196-245-135.netcologne.de [213.196.245.135]) by mrbusi1.netcologne.de (Postfix) with ESMTP id 5BFB41A0137; Tue, 5 Apr 2005 12:48:12 +0200 (CEST) Message-ID: <42526CEC.40000 <> cosmologic.de> Date: Tue, 05 Apr 2005 12:48:12 +0200 From: Andreas Klamt cosmologic.de> User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jelena Tamuliene mserv.itpa.lt> Cc: archilles02 <> gmail.com, "chemistry <> ccl.net" ccl.net> Subject: Re: CCL:W:problem with solvent effect calculations (fwd) References: <20050321162821.S57161 <> mserv.itpa.lt> <20050322075517.E70623 <> mserv.itpa.lt> <423FB6AE.1020704 <> cosmologic.de> <20050322083449.F71600 <> mserv.itpa.lt> In-Reply-To: <20050322083449.F71600 <> mserv.itpa.lt> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear Jelena, as agreed on we did the TURBOMOLE/COSMO optimization of the geometry optimization of your large bioorganic molecule supramolecular structure, which you had problems with using PCM and Gaussian. As expected, the geometry optimization was no technical problem. It converged from your start structure without any problem. The complex had NUMBER OF ATOMS: 112 DEGREES OF FREEDOM: 330 INTERNAL COORDINATES: 379 We performed a BP DFTcalculation with TZVP basis set resulting in 1413 atom orbitals. The calculation took about 9 days on a single 3MHz CPU. It took 145 geometry optimization steps. As a result we may conclude, that optimization of such complexes with the dielectric continuum solvation model COSMO is technically doable with no problems using TURBOMOLE. Obviously, such calculations are for such floppy supramolecular complexes are time consuming. Best regards Andreas Jelena Tamuliene wrote: > > Dear Professor Klamt, > > Thank you for your letter. > Of course we agree. > > Thank you again. > > With respect, > > Jelena > > On Tue, 22 Mar 2005, Andreas Klamt wrote: > >> Dear Jelena, >> >> we will be happy to do it, but with our default level BP91 and TZVP >> basis set. The geometries typically depend very little on the DFT >> method. So a well optimized BP91/TZVP optimization should be o.k. for >> your applications. And TURBOMOLE is so much faster for non-hybride >> functionals due to the RI approximation. >> >> If you agree please let me know. >> >> Andreas >> >> Jelena Tamuliene wrote: >> >>> >>> Dear Professor Klamt, >>> >>> Thank you for your help. >>> Please find attached the coordinates of the derivatives that we >>> would like to optimize in water solvent. It will be very kind of you >>> to perform the optimization by DFT method PBEPBE or B3PW91 approch >>> with 6-31+G** basis set. >>> Thank you in advance. >>> With respect, >>> >>> J. Tamuliene >>> ************************************************************************** >>> Research Fellow >>> Vilnius University Institute of Theoretical Physics and Astronomy >>> A. Gostauto 12, LT-01108 Vilnius >>> Lithuania >>> >>> Phone: 370-5-2620861 >>> Fax: 370-5-2125361 >>> E-mail: gicevic <> itpa.lt >>> >>> *************************************************************************** >>> >>> >>>> >>>> Dear Arvydas Tamulis, Noel O'Boyle and other CCL Colleagues, >>>> >>>> while I do not have much experience with PCM optimization in >>>> Gaussian, I can definitely say, that my COSMO in TURBOMOLE is very >>>> robust and efficien even for geometry optimization of large >>>> molecules. I suggest that you let us have a typical start structure >>>> and we try an optimization here. We will communicate the results >>>> via CCL. >>>> >>>> Andreas >>>> >>>> -- >>>> >>>> ----------------------------------------------------------------------------- >>>> Dr. habil. Andreas Klamt >>>> COSMOlogic GmbH&CoKG >>>> Burscheider Str. 515 >>>> 51381 Leverkusen, Germany >>>> >>>> Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 >>>> e-mail: klamt <> cosmologic.de >>>> web: www.cosmologic.de >>>> >>>> ----------------------------------------------------------------------------- >>>> COSMOlogic >>>> Your Competent Partner for >>>> Computational Chemistry and Fluid Thermodynamics >>>> >>>> ----------------------------------------------------------------------------- >>>> >>>> >>>> >>>> Arvydas Tamulis wrote: >>>> >>>>> Dear Noel O'Boyle and other CCL Colleagues, >>>>> >>>>> I have never succeeded to get G03 optimization using PCM or iefpcm >>>>> of large >>>>> bioorganic molecule, supermolecular or supramolecular structures >>>>> indeed. >>>>> In the case if somebody else know how to to do this you are >>>>> welcome to teach me. >>>>> >>>>> Let me correct Noel O'Boyle's sheme of calculations with PCM or >>>>> iefpcm. >>>>> >>>>> In the case if you will optimize geometry of large bioorganic >>>>> molecule, supermolecular or supramolecular structure in the vaacum >>>>> you will >>>>> get not correct mutual displacement. That will not allow later to >>>>> get good >>>>> single point calculations with PCM or iefpcm. >>>>> >>>>> We are doing geometry optimization of large bioorganic >>>>> molecule, supermolecular or supramolecular structures together >>>>> with surrounding H2O molecules shell. We remove H2O molecules and >>>>> only then doing calculations with PCM or iefpcm of large bioorganic >>>>> molecule, supermolecular or supramolecular structures. >>>>> >>>>> Best regards, >>>>> Arvydas Tamulis >>>>> www.itpa.lt/~tamulis/ ****************************************** >>>>> >>>>> On Wed, 16 Mar 2005, Girish Ssr Suravajhula wrote: >>>>> >>>>>> >>>>>> ----- Forwarded message from noel.oboyle2 <> mail.dcu.ie ----- >>>>>> Date: Tue, 15 Mar 2005 08:56:10 +0000 >>>>>> From: Noel O'Boyle mail.dcu.ie> >>>>>> Reply-To: noel.oboyle <> ucd.ie >>>>>> Subject: Re: CCL:W:problem with solvent effect calculations >>>>>> To: "girish, s, suravajhula" latech.edu> >>>>>> >>>>>> You need to geometry optimise the structure first, starting with a >>>>>> structure that Gaussian does correctly understand. You don't need >>>>>> to use >>>>>> PCM for this step. After this, geometry with PCM (if possible) or >>>>>> just >>>>>> do a single-point calculation with PCM. >>>>>> >>>>>> Regards, >>>>>> Noel >>>>>> >>>>>> On Mon, 2005-03-14 at 17:57, girish, s, suravajhula wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I was trying to perform solvent effect calculations on >>>>>>> calix[4]arene crown-6 >>>>>> >>>>>> >>>>>> >>>>>> interaction with cesium in chcl3 as solvent. >>>>>> >>>>>>> >>>>>>> For that I placed cesium inside the crown structure did the PCM >>>>>>> calculations >>>>>>> >>>>>>> But guassian gave me an error. What its actually doing is >>>>>>> counting the number >>>>>> >>>>>> >>>>>> >>>>>> if bonds cesium is formin with all the surrounding atoms. And >>>>>> since cesium is >>>>>> very close to many atoms its showing errors like Hydrogen has two >>>>>> bonds. >>>>>> >>>>>>> >>>>>>> could any one suggenst me how to correct this error. >>>>>>> >>>>>>> I would be glad if any one can suggest me any other method how I >>>>>>> should >>>>>> >>>>>> >>>>>> >>>>>> perform a solvent effect on calix[4]arene crown-6 and cesium with >>>>>> chcl3 as the >>>>>> solvent. >>>>>> >>>>>>> >>>>>>> Regards. >>>>>>> >>>>>>> Girish Suravajhula. >>>>>>> >>>>>>> >>>>>>> To send e-mail to subscribers of CCL put the string CCL: on your >>>>>>> Subject: line >>>>>>> >>>>>>> Send your subscription/unsubscription requests to: >>>>>>> CHEMISTRY-REQUEST <> ccl.net >>>>>>> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ----- End forwarded message ----- >>>>>> >>>>>> >>>>>> ---------------------------------------------------------------- >>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>> >>>>> >>>>> >>>>> To send e-mail to subscribers of CCL put the string CCL: on your >>>>> Subject: line >>>>> and send your message to: CHEMISTRY <> ccl.net >>>>> >>>>> Send your subscription/unsubscription requests to: >>>>> CHEMISTRY-REQUEST <> ccl.net HOME Page: http://www.ccl.net | Jobs >>>>> Page: http://www.ccl.net/jobs >>>>> Jan Labanowski, jlabanow <> nd.edu (read about it on CCL Home Page) >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> >>>> -= This is automatically added to each message by the mailing >>>> script =- >>>> To send e-mail to subscribers of CCL put the string CCL: on your >>>> Subject: line >>>> and send your message to: CHEMISTRY <> ccl.net >>>> >>>> Send your subscription/unsubscription requests to: >>>> CHEMISTRY-REQUEST <> ccl.net HOME Page: http://www.ccl.net | Jobs >>>> Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET >>>> domain send it to the maintainer: >>>> Jan Labanowski, jlabanow <> nd.edu (read about it on CCL Home Page) >>>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >>>> >>>> >>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> >>> >>> C -5.785353 -2.228004 -1.689626 >>> N -5.010075 -1.150248 -2.224425 >>> C -3.699579 -1.320343 -2.563354 >>> C -3.109345 -2.544660 -2.479830 >>> C -3.926052 -3.621260 -2.009317 >>> N -5.200146 -3.459244 -1.650000 >>> C -5.630462 0.172775 -2.295998 >>> C -4.978835 1.207667 -1.380149 >>> O -3.993791 1.852499 -1.820088 >>> N -3.422058 -4.878440 -1.914356 >>> O -6.954957 -1.987828 -1.299134 >>> N -5.523126 1.487035 -0.150971 >>> C -4.902880 2.601484 0.596306 >>> C -5.275090 3.989602 0.051441 >>> N -4.509067 5.006982 0.754937 >>> C -6.437089 0.572903 0.559628 >>> C -7.812709 1.201325 0.825784 >>> O -8.507819 0.844136 1.803468 >>> C -5.871084 0.023616 1.875350 >>> C -4.589688 -0.763961 1.705569 >>> O -4.166982 -1.146647 0.594791 >>> N -3.934230 -1.059018 2.873892 >>> C -2.698590 -1.846054 2.905204 >>> N -1.469327 -1.070377 3.061173 >>> C -1.353567 -0.358296 4.331506 >>> C -0.972661 -0.415722 1.891753 >>> C -0.310708 -1.198250 0.888144 >>> C 0.104555 -0.575658 -0.335848 >>> C -0.049582 0.844257 -0.498865 >>> C -0.644429 1.570007 0.520529 >>> C -1.117913 0.944449 1.692900 >>> C 0.635396 -1.394868 -1.368213 >>> C 0.835830 -2.748454 -1.176598 >>> C 0.519130 -3.342650 0.068246 >>> C -0.051784 -2.583730 1.070198 >>> N 0.386162 1.457980 -1.701776 >>> C -0.359642 2.623812 -2.169598 >>> C 1.834318 1.571963 -1.912350 >>> N -8.236656 2.106904 -0.096561 >>> C -9.580931 2.678668 -0.073841 >>> C -10.496440 2.072639 -1.139266 >>> C 4.857283 -0.674649 2.164412 >>> C 6.226208 -0.494894 1.961274 >>> C 6.830129 -0.939728 0.772399 >>> C 6.039423 -1.566447 -0.206455 >>> C 4.674422 -1.747697 0.000182 >>> C 4.078888 -1.301892 1.186558 >>> C 8.278581 -0.774380 0.500894 >>> C 9.143920 -0.139064 1.581032 >>> O 10.539962 -0.190744 1.209174 >>> C 10.978527 0.786537 0.331415 >>> C 12.369199 0.488174 -0.144061 >>> C 13.028109 1.665639 -0.863589 >>> C 14.417368 1.314552 -1.411403 >>> C 15.087102 2.493117 -2.124473 >>> O 8.789546 -1.134064 -0.573024 >>> O 10.282427 1.754420 0.023021 >>> H -7.605582 2.350561 -0.845732 >>> H -6.621488 -0.299412 -0.087346 >>> H -3.562903 5.150930 0.433265 >>> H -4.990272 5.861682 0.986686 >>> H -5.116739 3.999505 -1.037819 >>> H -6.339906 4.169688 0.235254 >>> H -3.815271 2.481734 0.556181 >>> H -5.216818 2.548935 1.639461 >>> H -6.691924 0.016552 -2.099045 >>> H -5.505164 0.567408 -3.308759 >>> H -4.030223 -5.602226 -1.568123 >>> H -2.463563 -5.087422 -2.128250 >>> H -2.064537 -2.676571 -2.724488 >>> H -3.169957 -0.429102 -2.877331 >>> H -9.505997 3.765681 -0.201915 >>> H -10.102505 2.240263 -2.148697 >>> H -10.598727 0.993782 -0.986864 >>> H -4.334736 -0.747009 3.745982 >>> H -5.731101 0.821953 2.613966 >>> H -6.649775 -0.626243 2.294503 >>> H -2.657189 -2.392382 1.961765 >>> H -2.765800 -2.554938 3.737531 >>> H -1.612578 1.550053 2.445575 >>> H -0.762381 2.643093 0.416265 >>> H 0.857071 -0.930947 -2.322957 >>> H 1.240517 -3.357599 -1.980198 >>> H 0.720982 -4.397063 0.232403 >>> H -0.299227 -3.024582 2.029783 >>> H -0.347711 0.058842 4.422839 >>> H -2.076869 0.466291 4.455311 >>> H -1.507203 -1.067777 5.153295 >>> H 2.258515 2.447353 -1.388827 >>> H 2.344671 0.680226 -1.544173 >>> H 2.045611 1.679129 -2.982068 >>> H -0.146849 2.773100 -3.234261 >>> H -1.432126 2.451424 -2.050119 >>> H -0.084716 3.557866 -1.644394 >>> H -9.977932 2.483277 0.926239 >>> H -11.493638 2.524383 -1.087686 >>> H 6.522791 -1.900091 -1.118551 >>> H 4.067456 -2.232991 -0.756544 >>> H 3.014289 -1.442854 1.343186 >>> H 4.397069 -0.324920 3.082887 >>> H 6.813141 -0.001432 2.729575 >>> H 14.479515 2.837866 -2.969991 >>> H 15.219897 3.342330 -1.442975 >>> H 15.059941 0.970121 -0.587417 >>> H 14.329777 0.466241 -2.106307 >>> H 12.376348 1.998331 -1.681474 >>> H 13.106701 2.517637 -0.174266 >>> H 8.838059 0.902230 1.737313 >>> H 9.073450 -0.692084 2.520197 >>> H 12.965661 0.154540 0.714376 >>> H 12.294316 -0.382749 -0.812011 >>> H 16.074352 2.217054 -2.511644 >>> >>> >> >> >> -- >> ----------------------------------------------------------------------------- >> >> Dr. habil. Andreas Klamt >> COSMOlogic GmbH&CoKG >> Burscheider Str. 515 >> 51381 Leverkusen, Germany >> >> Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 >> e-mail: klamt <> cosmologic.de >> web: www.cosmologic.de >> ----------------------------------------------------------------------------- >> >> COSMOlogic >> Your Competent Partner for >> Computational Chemistry and Fluid Thermodynamics >> ----------------------------------------------------------------------------- >> >> >> >> > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt <> cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From chemistry-request@ccl.net Tue Apr 5 15:07:56 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j35J7t5x024957 for ; Tue, 5 Apr 2005 15:07:55 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j35J7tk8024956 for chemistry$at$ccl.net; Tue, 5 Apr 2005 15:07:55 -0400 Date: Tue, 5 Apr 2005 15:07:55 -0400 Message-Id: <200504051907.j35J7tk8024956$at$server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request$at$ccl.net using -f From: "Attila, , Borics" To: chemistry$at$ccl.net X-Web-Message-Number: 050405150645-24887 Subject: W:Solvation models in Gaussian 03 X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear CCL readers, I do geometry optimizations on ~60 atom systems using B3LYP and B3PW91 hybrid functionals on the 6-31G* basis set. I do gas phase optimizations without any problem, but when it comes to SCRF solvation (DMSO, CDCl3, etc.), my jobs often crash, with error messages like: AdVTs1: ISph= 830 is engulfed by JSph= 831 but Ae( 830) is not yet zero! Error termination via Lnk1e in /usr/local//g03/l301.exe at Sun Feb 27 01:15:48 2005. or BldSpC: Error generating genealogic tree for sphere 894 at level 15 Error termination via Lnk1e in /usr/local//g03/l301.exe at Sat Feb 26 09:50:34 2005. I believe this is related to the solvation model. Another interesting feature of these solvated optimizations is that when it completed without error it resulted in almost identical final structure as in gas phase (with identical initial structures), which is, however, possible but unlikely considering a 4 residue peptide. Frequency calculations, howewer, on the almost superimposable output structures revealed major differences, not only in frequencies, but IR intensities and rotational strengths. Interestingly, gas phase calculations reproduced experimental results better, than optimizations utilizing the SCRF method. So, my question is how good or reliable is this SCRF method incorporated in G03? Is there any reliable solvation model within G03? What do you suggest? Thank You Attila Borics From chemistry-request@ccl.net Tue Apr 5 15:02:28 2005 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j35J2IeU024703 for ; Tue, 5 Apr 2005 15:02:22 -0400 Received: (from www@localhost) by alchemy.chem.utoronto.ca (8.11.6/8.11.6) id j35HopX02573; Tue, 5 Apr 2005 13:50:51 -0400 X-Authentication-Warning: alchemy.chem.utoronto.ca: www set sender to mstaikov!at!chem.utoronto.ca using -f Received: from 142.150.225.11 ( [142.150.225.11]) as user mstaikov!at!alchemy.chem.utoronto.ca by mail.chem.utoronto.ca with HTTP; Tue, 5 Apr 2005 13:50:50 -0400 Message-ID: <1112723450.4252cffa953af!at!mail.chem.utoronto.ca> Date: Tue, 5 Apr 2005 13:50:50 -0400 From: "Mima G. Staikova" To: Cherif Matta Cc: chemistry!at!ccl.net, help!at!gaussian.com, Russell Boyd , Norberto Castillo Subject: Re: CCL:Gaussian03 Disk Space Error in MP2 References: <57ffe604158f.425007dd!at!jhumail.jhu.edu> <1112677533.42521c9d1d24c!at!my3.dal.ca> In-Reply-To: <1112677533.42521c9d1d24c!at!my3.dal.ca> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 142.150.225.11 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi Cherif, you can try and split the .rwf files in smaller that 2 GB increments, 1.9 is good. As well, try to monitor your .rwf in the scratch directory during calculation to see at what point the jobs is terminated. Regards, Mima Staikova Quoting Cherif Matta : > Dear all, > > We are trying to perform a single point calculation on a fairly large > system > using G03. We have a disk-space error in spite of the availability of much > more > free disk space than required in the error message. > > This is a neutral closed-shell system with 1014 basis functions, 1548 > primitive > gaussians, and 272 electrons. We are running it on a 64-bit SuSe9.1 Linux > Box > with 100 GB empty disk space. Since this is not a 32-bits system, the file > size should not be a problem. > > The following is the Gaussian03 input line: > ============================================ > #p MP2(full, verystingy)/6-311++g** output=wfn density=current > MaxDisk=65GB scf=(MaxCycle=200, tight) 6d 10f > > After the convergence of the SCF, the job is aborted, and > the following is the error we get: > ================================== > Cycle 2 Pass 1 IDiag 1: > RMSU= 4.56D-08 CP: 1.00D+00 > E= -1864.55241471435 Delta-E= -0.000000000020 Rises=F Damp=F > DIIS: error= 1.72D-09 at cycle 2 NSaved= 2. > NSaved= 2 IEnMin= 2 EnMin= -1864.55241471435 IErMin= 2 ErrMin= > 1.72D-09 > ErrMax= 1.72D-09 EMaxC= 1.00D-01 BMatC= 9.11D-16 BMatP= 1.96D-14 > IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 > Coeff-Com: 0.195D-01 0.980D+00 > Coeff: 0.195D-01 0.980D+00 > Gap= 0.295 Goal= None Shift= 0.000 > RMSDP=6.47D-09 MaxDP=6.88D-07 DE=-2.00D-11 OVMax= 5.82D-09 > > SCF Done: E(RHF) = -1864.55241471 A.U. after 2 cycles > Convg = 0.6466D-08 -V/T = 2.0011 > S**2 = 0.0000 > KE= 1.862590819875D+03 PE=-1.379542208284D+04 EE= 5.357304786856D+03 > Leave Link 502 at Sat Apr 2 04:00:29 2005, MaxMem= 31457280 cpu: > 11736.6 > (Enter /home/programs/g03/l801.exe) > Range of M.O.s used for correlation: 1 1009 > NBasis= 1014 NAE= 136 NBE= 136 NFC= 0 NFV= 0 > NROrb= 1009 NOA= 136 NOB= 136 NVA= 873 NVB= 873 > > **** Warning!!: The largest alpha MO coefficient is 0.13325828D+03 > > Leave Link 801 at Sat Apr 2 04:00:29 2005, MaxMem= 31457280 cpu: > 0.1 > (Enter /home/programs/g03/l906.exe) > Not enough disk for semidirect, minimum= 946930225 > Not enough memory for fully direct, minimum= 141181640. > Not enough resources for E2 calculation. > Error termination via Lnk1e in /home/programs/g03/l906.exe at Sat Apr 2 > 04:00:30 2005. > ======================================================== > > We tried to run the job on a cluster with RedHat Linux where the scratch > files > were broken, each into 6 x 2GB-files, but we got exactly the same error > message > despite the availability of a huge disk space. > > Can someone help with this? I will summarize. > > Thank you very much in advance. > > Cheers, > > Cherif > > ------------------------------------------------------- > Cherif F. Matta, Ph.D., MCIC > * Izaak Walton Killam Post Doctoral Fellow > Department of Chemistry, Dalhousie University > Halifax, NS, Canada. > * Adjunct Professor of Chemistry > McMaster University, Hamilton, ON, Canada. > ------------------------------------------------------- > * Web site: http://chem.utoronto.ca/~cmatta/ > Tel: (902) 494 7021 Fax: (902) 494 1310 > ------------------------------------------------------- > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY!at!ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST!at!ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- Mima G. Staikova Ph.D. Department of Chemistry Undergraduate Computer Lab 80 St. George Street University of Toronto Toronto, Ontario M5S 3H6 phone: (416) 978-1388 email: mstaikov!at!chem.utoronto.ca ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From chemistry-request@ccl.net Tue Apr 5 19:21:29 2005 Received: from molsoft.com (mail.molsoft.com [64.186.242.98]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j35NLPsJ006328 for ; Tue, 5 Apr 2005 19:21:25 -0400 Received: from vega.molsoft.com (vega.molsoft.com [64.186.242.119]) by molsoft.com (8.12.8/8.12.8) with ESMTP id j35LdwTF006417 for ; Tue, 5 Apr 2005 14:40:02 -0700 Date: Tue, 5 Apr 2005 14:39:58 -0700 (PDT) From: Molsoft LLC To: chemistry)at(ccl.net Subject: Molsoft ICM Workshop Cambridge MA In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net LIMITED SPACES ARE AVAILABLE at our East Coast Workshop in Cambridge MA. 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