From chemistry-request@server.ccl.net Wed Oct 16 01:24:48 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9G5Omf31909 for ; Wed, 16 Oct 2002 01:24:48 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 74D54913A; Wed, 16 Oct 2002 07:24:48 +0200 (CEST) To: chemistry@ccl.net Subject: IRC on sugar Message-ID: <1034745888.3dacf82068b4a@webmail.u-picardie.fr> Date: Wed, 16 Oct 2002 07:24:48 +0200 (CEST) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, Do you have reference(s) of intrinsec reaction coordinate (IRC) calculations realized on a sugar (glucose, galactose, mannose...) in comparison to cyclohexane ? Thanks, regards, Francois From chemistry-request@server.ccl.net Wed Oct 16 03:28:04 2002 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9G7S4f01384 for ; Wed, 16 Oct 2002 03:28:04 -0400 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id JAA17197 for ; Wed, 16 Oct 2002 09:27:29 +0200 (MEST) Message-ID: <3DAD156E.8C8E625A@fy.chalmers.se> Date: Wed, 16 Oct 2002 09:29:50 +0200 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: AIM errors in G98 References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all Have just started to try out AIM analysis using G98. I do get strange errors (not the ones listed in the g98 users ref.) even for simple(?) cases like the BF4- anion... Error messages: >> DUPLICATE CRITICAL POINTS FOUND 82 77 >> TOO MANY INTERSECTIONS Anyone knows how to alter to make it work?? /Patrik -- Patrik Johansson (patrikj@fy.chalmers.se) Scientist @ Materials Physics Group Chalmers University of Technology 412 96 Goteborg SWEDEN NEW!!! http://fy.chalmers.se/mf/Computer.html http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Wed Oct 16 05:06:49 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9G96nf03540 for ; Wed, 16 Oct 2002 05:06:49 -0400 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id g9G968mY012783; Wed, 16 Oct 2002 11:06:08 +0200 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id g9G967dl012780; Wed, 16 Oct 2002 11:06:07 +0200 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Wed, 16 Oct 2002 11:06:07 +0200 (CEST) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: "Panagiotis G. Karamertzanis" cc: CHEMISTRY@ccl.net Subject: Re: CCL:Gamess question In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g9G96nf03541 Hi, Gamess units are Atomic Units o Hartrees, indicated also as AU 1 AU is equivalent to: 27.2107 eV 4.35943E-11 erg 6.27503E+2 Kcal/mol 6.57966E+15 Hz 2.19474E+05 cm-1 3.15777E+05 K Cheers Alessandro Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Tue, 15 Oct 2002, Panagiotis G. Karamertzanis wrote: > Dear all, > > I started using GAMESS recently. I am computing electrostatic potential to > do later on fitting with distributed charges. > > The problem is that I do not know the units of the output of the GAMESS run. > The manual does not help with this. > > Thanks, > > Panagiotis Karamertzanis > CPSE Imperial College > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed Oct 16 06:32:25 2002 Received: from relay.unizar.es ([155.210.11.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9GAWMf04653 for ; Wed, 16 Oct 2002 06:32:22 -0400 Received: from there ([155.210.93.83]) by relay.unizar.es (8.12.6/8.12.3) with SMTP id g9GAQlIC029840 for ; Wed, 16 Oct 2002 12:26:52 +0200 Message-Id: <200210161026.g9GAQlIC029840@relay.unizar.es> Content-Type: text/plain; charset="iso-8859-1" From: Santiago Cuesta <405137@docto.unizar.es> Reply-To: 405137@docto.unizar.es Organization: Ciencias To: chemistry@ccl.net Subject: CHARMM parameters FAD+ Date: Wed, 16 Oct 2002 12:25:58 +0200 X-Mailer: KMail [version 1.3.2] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Hi everybody !!! We are trying to determinate some structural mechanism in flavoproteins involving FAD and NADP ... as a part of our study, we need to perform a Molecular Dynamics calculation using CHARMM (academic version c27b4)... Our problem is that FAD parameters aren't included in our package ( Isoalloxazine, Riboflavine ...) and we haven't found them anywhere, so we would be very grateful if someone could suggest us any idea ... Are new files containing Flavine parameters available?? It's possible to obtain them in a different format to adapt CHARMM....??? Do you know about any reference (paper, published calculation ...) ??? Thanks in advance for your help Regards Santiago Cuesta -------------------------------------------------------------------------- Santiago Cuesta López Ph.D. student Dep. Física de la Materia Condensada. Dep. Teoria y Simulacion de Sistemas Complejos (ICMA-CSIC) Universidad de Zaragoza. (Spain) From chemistry-request@server.ccl.net Wed Oct 16 04:07:46 2002 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9G87jf02535 for ; Wed, 16 Oct 2002 04:07:45 -0400 Received: (qmail 24357 invoked from network); 16 Oct 2002 08:07:37 -0000 Received: from mistral.itqb.unl.pt (herrmann@193.136.176.14) by gatekeeper.itqb.unl.pt with SMTP; 16 Oct 2002 08:07:37 -0000 Received: from localhost (herrmann@localhost) by mistral.itqb.unl.pt (8.9.3/8.9.3) with ESMTP id JAA06983 for ; Wed, 16 Oct 2002 09:07:36 +0100 Date: Wed, 16 Oct 2002 09:07:36 +0100 (WEST) From: Rudolf Herrmann To: chemistry@ccl.net Subject: Summary: G98: VOVl3 problem: convergence criterion not met In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, here is the summary of all the answers I got for my problem. Thanks (in alphabetically order) to Laurence Cuffe, Kerwin Dobbs, Paul Kiprof, Liviu Mirica, Cory Pye and Dave Shobe. The problem was solved by increasing the number of SCF cycles, as suggested by many. This seems very often necessary with transition metals. The two other suggestions (using first a small basis set before switching to the larger, or turning off "vshift", did not work, unfortunately. Thanks again, R.Herrmann. The original question: ---------------------------------------------------------------------------- Hello, I recently tried to calculate the NMR chemical shifts of VOCl3 with Gaussian 98: --------------------- #B3LYP/6-31G* SP NMR VOCl3 0 1 cl cl 1 clcl2 cl 2 clcl3 1 clclcl3 o 3 ocl4 2 oclcl4 1 dih4 v 3 vcl5 2 vclcl5 1 dih5 clcl3 3.506243 clclcl3 59.999 ocl4 2.938735 oclcl4 53.376 dih4 -64.586 vcl5 2.118170 vclcl5 34.144 dih5 -31.640 ----------------------- The result (even with several variations in the input) is always an error termination when trying the "incremental Fock formation" (convergence criterion not met). The structure was optimized with GAMESS. Any suggestion what I could do is wellcome - thank you! ------------------------------ 108 basis functions 288 primitive gaussians 41 alpha electrons 41 beta electrons nuclear repulsion energy 561.9817715949 Hartrees. One-electron integrals computed using PRISM. NBasis= 108 RedAO= T NBF= 108 NBsUse= 108 1.00D-04 NBFU= 108 Projected Huckel Guess. Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Virtual orbitals will be shifted by 0.200 hartree. Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RB+HF-LYP) = -2359.59549049 A.U. after 65 cycles Convg = 0.5851D-03 -V/T = 1.9657 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/local/g98_a7/l502.exe. Job cpu time: 0 days 0 hours 16 minutes 33.0 seconds. File lengths (MBytes): RWF= 14 Int= 0 D2E= 0 Chk= 1 Scr= 1 -------------------------------------------------------------------------- The answers: 1. From: Kerwin D Dobbs To: "Rudolf Herrmann Subject: Re: CCL:G98: VOCl3 problem: convergence criterion not met Dr. Herrmann, Try turning off the "vshift" by changing the line, #B3LYP/6-31G* SP NMR to # B3LYP/6-31G* SP NMR IOP(5/10=-1) When there is a TM in the molecule, G98 automatically turns on "VSHIFT" which usually makes SCF convergence worse. The above addition to your line turns off "VSHIFT". Give it a try and see what happens. Kerwin ------------------------------------------------------------------ 2. From: Cory Pye To: Rudolf Herrmann Subject: Re: CCL:G98: VOCl3 problem: convergence criterion not met Hello, your SCF is not converging. Try running, at first, HF/STO-3G. If it works, then Then try B3LYP/6-31G* afterwards with guess=read in the input. It usually works like a charm for me, I always use something like this. -Cory ---------------------------------------------------------------------- 3. From: Liviu Mihail Mirica To: Rudolf Herrmann Subject: Re: CCL:G98: VOCl3 problem: convergence criterion not met Try adding SCFcyc=1000 in your command lines. This will increase the # of SCF cycles up to the desired number (1000 in this case). that should be enough for your system. ------------------------------------------------------------------------ 4. From: Laurence Cuffe To: Rudolf Herrmann Subject: Re: CCL:G98: VOCl3 problem: convergence criterion not met And it should run these keywords change the default SCF method and then increase the number of SCF cycles allowed. I got the job to complete in about 50 minutes running it in core on a linux box with a memory limit of 600MB but it this doesn't make sense to you don't worry about it. Try using the modified line above and if there are any problems don't hesitate to come back to me. All the best Laurence Cuffe ------------------------------------------------------------------------- 5. From: Paul Kiprof To: herrmann@itqb.unl.pt Subject: VOCL3 Dear Dr. Herrmann, I would add to the input SCF(direct,qc,maxcycle=1000) This will increase the number of convergence cycles and hopefully converge the calculation. I always do that when I have transition metal compounds. Best wishes, Paul Kiprof --------------------------------------------------------------------------- 6. From: "Shobe, Dave" To: 'Rudolf Herrmann' Subject: RE: G98: VOCl3 problem: convergence criterion not met The standard 64 SCF "cycles" (or iterations of the variational procedure) is rarely enough for transition metal compounds, even closed shell ones like VOCl3. Read the section in the Gaussian manual describing the "scf" keyword, and you will find various options which may improve the convergence. A lot of it is trial and error, with these different scf options. The simplest is scf(maxcyc=999) which increases the number of cycles/iterations to 999 before the program "gives up" and prints the error message. Scf=qc and scf(vshift=###) have also been useful in my experience. More advice: once you get a good wavefunction, make a backup of the checkpoint file, so if the wave function becomes corrupted in subsequent calculations you can always go back to it. ---------------------------------------------------------------------------- -- Dr. Rudolf Herrmann Instituto de Tecnologia Quimica e Biologica (ITQB) Av. da Republica, EAN, Apt. 127 P-2781-901 Oeiras e-mail: herrmann@itqb.unl.pt From chemistry-request@server.ccl.net Wed Oct 16 01:10:22 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9G5ALf31679 for ; Wed, 16 Oct 2002 01:10:21 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id D7F94913A; Wed, 16 Oct 2002 07:10:17 +0200 (CEST) To: chemistry@ccl.net Subject: GAMESS error message Message-ID: <1034745017.3dacf4b9cba25@webmail.u-picardie.fr> Date: Wed, 16 Oct 2002 07:10:17 +0200 (CEST) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I run the following input in GAMESS on an alpha (TRU64/OSF1) on TWO processors: $CONTRL RUNTYP=SADPOINT SCFTYP=RHF EXETYP=RUN $END $SYSTEM TIMLIM=10000 MWORDS=105 MEMDDI=0 $END $STATPT NSTEP=100 OPTTOL=0.0001 HESS=CALC IHREP=7 $END $FORCE METHOD=ANALYTIC VIBANL=.F. $END I get the following error message: ********************************************************************** THE HESSIAN WILL NOW BE RECOMPUTED FROM SCRATCH. ********************************************************************** ...... END OF ONE-ELECTRON INTEGRALS ...... ON NODE 0, STEP CPU TIME = 0.21 TOTAL CPU TIME = 6543.6 ( 109.1 MIN) TOTAL WALL CLOCK TIME= 14538.0 SECONDS, CPU UTILIZATION IS 45.01% TOTAL NUMBER OF NONZERO TWO-ELECTRON INTEGRALS = 200208052 13349 INTEGRAL RECORDS WERE STORED ON DISK FILE 8. ...... END OF TWO-ELECTRON INTEGRALS ..... ON NODE 0, STEP CPU TIME = 52.79 TOTAL CPU TIME = 6596.4 ( 109.9 MIN) TOTAL WALL CLOCK TIME= 14622.0 SECONDS, CPU UTILIZATION IS 45.11% -------------------------- RHF SCF CALCULATION -------------------------- DENSITY MATRIX CONV= 1.00E-05 ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD ---------------START SECOND ORDER SCF--------------- 1 0 0 -724.396486456 -724.396486456 0.028879580 0.007240184 .... 10 9 0 -724.401504597 0.000000000 0.000000369 0.000000141 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 105.3 SECONDS ( 10.5 SEC/ITER) TIME TO SOLVE SCF EQUATIONS= 1.6 SECONDS ( 0.2 SEC/ITER) FINAL RHF ENERGY IS -724.4015045968 AFTER 10 ITERATIONS ...... END OF RHF CALCULATION ...... ON NODE 0, STEP CPU TIME = 107.26 TOTAL CPU TIME = 6703.6 ( 111.7 MIN) TOTAL WALL CLOCK TIME= 15278.0 SECONDS, CPU UTILIZATION IS 43.88% GENERATING REPLICATED AO INTEGRAL LISTS FOR THE TRANSFORMATION STEP. TOTAL NUMBER OF NONZERO TWO-ELECTRON INTEGRALS = 200208052 13348 INTEGRAL RECORDS WERE STORED ON DISK FILE 8. ...... END OF TWO-ELECTRON INTEGRALS ..... STEP CPU TIME = 102.48 TOTAL CPU TIME = 6806.1 ( 113.4 MIN) TOTAL WALL CLOCK TIME= 15457.0 SECONDS, CPU UTILIZATION IS 44.03% ...... END OF 1-ELECTRON GRAD+HESS+FOCKDER ...... ON NODE 0, STEP CPU TIME = 542.19 TOTAL CPU TIME = 7348.3 ( 122.5 MIN) TOTAL WALL CLOCK TIME= 17422.0 SECONDS, CPU UTILIZATION IS 42.18% THE COARSE/FINE SCHWARZ SCREENINGS SKIPPED 4280058/ 393668 BLOCKS. THE NUMBER OF DERIVATIVE INTEGRAL BLOCKS COMPUTED WAS 2994894 ...... END OF 2-ELECTRON GRAD+HESS+FOCKDER ...... ON NODE 0, STEP CPU TIME = 1649.90 TOTAL CPU TIME = 8998.2 ( 150.0 MIN) TOTAL WALL CLOCK TIME= 19093.0 SECONDS, CPU UTILIZATION IS 47.13% SOLVING FOR 90 NUCLEAR RESPONSES AND 0 ELECTRIC FIELD RESPONSES ERROR READING FILE 16 ON NODE 0 LENGTH= 99363385 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Thu Oct 10 09:48:13 2002 104994774 WORDS OF DYNAMIC MEMORY USED STEP CPU TIME = 103.22 TOTAL CPU TIME = 9101.4 ( 151.7 MIN) TOTAL WALL CLOCK TIME= 20434.0 SECONDS, CPU UTILIZATION IS 44.54% *** ERROR TERMINATION *** IN COMPUTE PROCESS 0 Any idea ? Thanks, Regards, Francois From chemistry-request@server.ccl.net Wed Oct 16 05:21:59 2002 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9G9Lxf03773 for ; Wed, 16 Oct 2002 05:21:59 -0400 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id LAA28463; Wed, 16 Oct 2002 11:21:47 +0200 (MET DST) for From: cbiot@ulb.ac.be Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id LAA02126; Wed, 16 Oct 2002 11:21:47 +0200 (MET DST) for Message-ID: <3DAD2FD6.5000603@ulb.ac.be> Date: Wed, 16 Oct 2002 11:22:30 +0200 Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: Liste CCL Subject: with or without...... BSSE Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Folks, When performing an ab initio calculation of DeltaG(solvation) of complexes in solution (water, ethanol, DMSO, aso...), should I take into account the interaction energy with or without BSSE. Can anyone comment on what should be done to clarify this situation? Some bibliographic references will be greatly appreciated!! Best....& take care Christophe B -- ******************************************************* Dr. BIOT Christophe Ingenierie Biomoleculaire, CP 165/64 Universite Libre de Bruxelles 50, Av. F. Roosevelt B-1050 Bruxelles Belgique Phone: 32-2-650 3001 Fax: 32-2-650 3606 E-mail:cbiot@ulb.ac.be http://babylone.ulb.ac.be/~christophe/ http://www.ulb.ac.be/rech/inventaire/unites/ULB163.html ******************************************************* From chemistry-request@server.ccl.net Wed Oct 16 04:28:12 2002 Received: from cpimssmtpu01.email.msn.com ([207.46.181.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9G8SCf02868 for ; Wed, 16 Oct 2002 04:28:12 -0400 Received: from catchcafmsn ([68.129.118.166]) by cpimssmtpu01.email.msn.com with Microsoft SMTPSVC(5.0.2195.4905); Wed, 16 Oct 2002 01:26:53 -0700 Message-ID: <000d01c274ee$36dbad00$a6768144@com> Reply-To: "Mauricio Cafiero" From: "Mauricio Cafiero" To: Subject: error function Date: Wed, 16 Oct 2002 01:29:55 -0700 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-OriginalArrivalTime: 16 Oct 2002 08:26:53.0811 (UTC) FILETIME=[C867C430:01C274ED] hello: I was wondering if anyone could point me towards accurate code for the F0 (or error) function and its derivative. thanks Mauricio Cafiero Doctoral Candidate: Theoretical and Computational Quantum Chemistry University Of Arizona From chemistry-request@server.ccl.net Tue Oct 15 15:23:19 2002 Received: from TheWorld.com ([199.172.62.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9FJNIf11121 for ; Tue, 15 Oct 2002 15:23:18 -0400 Received: from world.std.com (bdc@world-f.std.com [199.172.62.5]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id PAA18040 for ; Tue, 15 Oct 2002 15:23:11 -0400 Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id PAA02005 for chemistry@ccl.net; Tue, 15 Oct 2002 15:23:01 -0400 (EDT) Date: Tue, 15 Oct 2002 15:23:01 -0400 (EDT) From: Joe M Leonard Message-Id: <200210151923.PAA02005@world.std.com> To: chemistry@ccl.net Subject: Macintosh questions I would welcome any guidance on the following questions (and assume somebody reading this has played with new Macintoshes): 1) What is the large-scale/floating point performance between the newest Macs and Intel machines? Is there any particular compilers and/or switches needed to realize max performance? 2) How does OSX compare to Linux as a development environment? Can one do C and Fortran coding (or more-modern languages) on these machines? Are there particular problem areas? 3) Is there any problem giving presentations from a Mac rather than a PC (both laptops)? Or, are the suitable video-out ports supported on each? Thanks in advance! Joe Leonard jle@theworld.com P.S. I figure our audience is sufficiently different to make "typical reviews" less than valuable :-).