From chemistry-request@server.ccl.net Tue Nov 28 17:11:03 2000 Received: from deliverator.sgi.com (deliverator.sgi.com [204.94.214.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA12027 for ; Tue, 28 Nov 2000 17:11:02 -0500 Received: from nodin.corp.sgi.com (fddi-nodin.corp.sgi.com [198.29.75.193]) by deliverator.sgi.com (980309.SGI.8.8.8-aspam-6.2/980310.SGI-aspam) via ESMTP id OAA22275; Tue, 28 Nov 2000 14:11:01 -0800 (PST) mail_from (godbout@sgihud.hudson.sgi.com) Received: from sgihud.hudson.sgi.com (sgihud.hudson.sgi.com [169.238.41.4]) by nodin.corp.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id OAA77388; Tue, 28 Nov 2000 14:10:30 -0800 (PST) Received: from arkham.hudson.sgi.com (arkham.hudson.sgi.com [169.238.41.21]) by sgihud.hudson.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id RAA93410; Tue, 28 Nov 2000 17:07:20 -0500 (EST) Received: from hudson.sgi.com (localhost [127.0.0.1]) by arkham.hudson.sgi.com (SGI-8.9.3/8.9.3) with ESMTP id OAA41430; Tue, 28 Nov 2000 14:09:52 -0800 (PST) Sender: godbout@arkham.hudson.sgi.com Message-ID: <3A242D2F.D42656CC@hudson.sgi.com> Date: Tue, 28 Nov 2000 14:09:51 -0800 From: Nathalie Godbout X-Mailer: Mozilla 4.73C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Sam Andersen CC: amber@cgl.ucsf.EDU, chemistry@ccl.net, godbout@sgihud.hudson.sgi.com Subject: Re: CCL:Performance of Compaq ES vs IBM or ORIGIN servers References: Content-Type: multipart/mixed; boundary="------------20FD6C770CBCC69F733ADB4F" This is a multi-part message in MIME format. --------------20FD6C770CBCC69F733ADB4F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sam Andersen wrote: > > Hi, > Does anybody have Compaq/DEC multiprocessor ALPHA servers that > are being used for MD simulations by AMBER or CHARMM using MPI > or any other parallel arch.? We are planning to buy 4 or 8 processor > ES40 or GS60 DEC server. This is for dedicated parallel processing > on all processors for MD simulations of large protein systems > (sizes of about 100K atoms). We have been using SGI-ORIGIN series > of machines for MD simulations and have NO experience with compaq > systems (for parallel jobs). > > Are there people in chemistry community using these servers > (under Tru64 UNIX and MPI/OPEMMP) for MD or other apps?. I would > appreciate if somebody comment on their efficeincy in parallel > jobs (particulalry SANDER or GIBBS of AMBER6). Also, if people > out there use other systems like multiprocessor SGI-ORIGIN or > IBM-SP2, Could you please comment on relative performance of > parallel execution of AMBER codes on these systems? If people > have expereinced particular probelms in running parallel jobs > (particularly AMBER6 MD simulations)on multiprocessor ES40 or > GS60 compaq/DEC systems, Please share your experience. > > I will post summary. > Thanks and happy thanksgiving weekend. > Sam > > Get FREE Email/Voicemail with 15MB at Lycos Communications at http://comm.lycos.com > Hi Sam, I've attached a text file with the timings for the prowat, dhfr and 4096wat Amber6 runs on sgi platforms including Origin architecture with up to 32 processors. Let me know if you have questions about these results. Nathalie -- ------------------------------------------------------------------------ Nathalie Godbout, Ph.D. SGI godbout@hudson.sgi.com Chemistry and Biology Applications Group (781)839-2147 One Cabot Road, Suite 250 (978)562-7450 fax Hudson, MA vnet:483-2147 01749, USA ------------------------------------------------------------------------ --------------20FD6C770CBCC69F733ADB4F Content-Type: text/plain; charset=us-ascii; name="results-amber6-ALL-all-platforms-orig-code-amber_mailing_list" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="results-amber6-ALL-all-platforms-orig-code-amber_mailing_list" Amber6/sander benchmarks across sgi platforms. Nathalie Godbout, sgi 11/28/00 *on sgi1400: - 4xPIII 500MHz/2048KB L2 cache - Linux - PGI compilers - MPICH (1.2) and sgi MPI *on sgi1200: - 16xPIII (8 nodes) 700MHz/256KB L2 cache - Linux - PGI compilers - MPICH (1.2) - ethernet (2 jobs/node) and myrinet (1 job/node) *on Origin200: - 4xR12k IP27 360MHz/4MB L2 cache - Irix 6.5.9 - MIPSpro 7.3.1 compilers - sgi MPI *on sgi2800: - 32xR12k IP27 400MHz/8MB L2 cache - Irix 6.5.9 - MIPSpro 7.3.1 compilers - sgi MPI *on sgi3800: - 128xR12k IP35 400MHz/8MB L2 cache - Irix 6.5.9 - MIPSpro 7.3.1 compilers - sgi MPI PROWAT: ------- sgi1400 sgi1400 sgi1200 sgi1200 origin200 (500mhz) (500mhz) (700mhz) (700mhz) (360mhz) mpich sgi-mpi ethernet myrinet ------------------------------------------------------------ nproc time spup time spup time spup time spup time spup 1 278.72 276.80 187.42 186.14 150.21 2 148 1.88 145 1.91 103 1.82 99 1.88 79 1.90 4 87 3.20 84 3.30 64 2.93 55 3.38 45 3.34 8 44 4.26 33 5.64 16 34 5.51 21 8.86 ------------------------------------------------------------ sgi2800 sgi3100 (400mhz) (400mhz) -------------------------------------------- nproc time spup %P time spup %P 1 136.20 133.82 2 71 1.92(95.83) 69 1.94(96.91) 4 39 3.49(95.13) 38 3.52(95.45) 8 22 6.19(95.82) 20 6.69(97.20) 16 13 10.48(96.49) 14 9.56(95.51) 32 11 12.38(94.89) 8 16.73(97.06) -------------------------------------------- DHFR: ----- sgi1400 sgi1400 sgi1200 sgi1200 origin200 (500mhz) (500mhz) (700mhz) (700mhz) (360mhz) mpich sgi-mpi ethernet myrinet ------------------------------------------------------------ nproc time spup time spup time spup time spup time spup 1 441.21 437.73 331.64 330.49 197.67 2 254 1.74 241 1.82 203 1.63 183 1.81 110 1.80 4 157 2.81 146 3.00 146 2.27 101 3.27 61 3.24 8 106 3.13 60 5.51 16 79 4.20 41 8.06 ------------------------------------------------------------ sgi2800 sgi3100 (400mhz) (400mhz) ------------------------------------------- nproc time spup %P time spup %P 1 166.47 163.20 2 94 1.77(87.01) 88 1.85(91.89) 4 51 3.26(92.43) 47 3.47(94.91) 8 30 5.55(93.69) 26 6.28(96.09) 16 20 8.32(93.85) 17 9.60(95.56) 32 18 9.25(92.07) 13 12.55(95.00) ------------------------------------------- 4096WAT: -------- sgi1400 sgi1400 sgi1200 sgi1200 origin200 (500mhz) (500mhz) (700mhz) (700mhz) (360mhz) mpich sgi-mpi ethernet myrinet ------------------------------------------------------------ nproc time spup time spup time spup time spup time spup 1 223.14 223.04 166.22 167.95 96.70 2 126 1.77 121 1.84 106 1.57 94 1.79 56 1.73 4 79 2.82 71 3.14 80 2.08 53 3.17 31 3.12 8 56 2.97 33 5.09 16 43 3.86 22 7.63 ------------------------------------------------------------ sgi2800 sgi3100 (400mhz) (400mhz) ------------------------------------------ nproc time spup %P time spup %P 1 85.44 84.18 2 45 1.90(94.74) 45 1.87(93.05) 4 24 3.56(95.88) 24 3.51(95.35) 8 14 6.10(95.55) 14 6.01(95.27) 16 10 8.54(94.18) 10 8.42(94.00) 32 9 9.49(92.35) 7 12.02(94.64) ------------------------------------------ spup is the abbreviation for speedup and %P is percentage of parallelism according to Amdhal's law. --------------20FD6C770CBCC69F733ADB4F-- From chemistry-request@server.ccl.net Wed Nov 29 07:25:29 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA16172 for ; Wed, 29 Nov 2000 07:25:28 -0500 Received: from gap.cco.caltech.edu (gap.cco.caltech.edu [131.215.139.43]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id HAA03060 for ; Wed, 29 Nov 2000 07:25:12 -0500 (EST) Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by gap.cco.caltech.edu (8.9.3/8.9.3) with ESMTP id EAA21871 for ; Wed, 29 Nov 2000 04:10:41 -0800 (PST) Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id NAA00952; Wed, 29 Nov 2000 13:10:00 +0100 X-Authentication-Warning: yogi.pc1.uni-duesseldorf.de: jochen set sender to jochen@pc1.uni-duesseldorf.de using -f Sender: jochen@pc1.uni-duesseldorf.de To: "Richard P. Muller" Cc: chemistry@ccl.net Subject: Re: CCL:visualizing vibrations References: <3A23F7C9.1C0BDA60@wag.caltech.edu> From: "Jochen =?iso-8859-1?q?K=FCpper?=" Organization: =?iso-8859-1?q?Heinrich-Heine-Universit=E4t?= Date: 29 Nov 2000 13:10:00 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit >>>>> Richard P Muller writes: Richard> Has anyone mentioned Moldens yet? It does a nice job of Richard> visualizing normal modes. Absolutely. Richard> Maybe someone can modify it to convert Gaussian modes. molden reads Gaussian files natively;-)) Greetings, Jochen -- Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43 Raum 02.29 GnuPG key: 44BCCD8E 40225 Düsseldorf, Germany phone ++49-211-8113681 http://www.Jochen-Kuepper.de fax ++49-211-8115195 From chemistry-request@server.ccl.net Wed Nov 29 12:38:30 2000 Received: from unlserve.unl.edu (unlserve.unl.edu [129.93.1.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA17405 for ; Wed, 29 Nov 2000 12:38:29 -0500 Received: from localhost (rrashid@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id LAA20778 for ; Wed, 29 Nov 2000 11:26:15 -0600 Date: Wed, 29 Nov 2000 11:26:15 -0600 (CST) From: Ali N Rashid To: chemistry@ccl.net Subject: Energy of Transition State is higher that ground state. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I user HF6-31+G* and 6-311+G+ to optimize the ground state of p-nitroamine. The amine come out pyramidal. When I hold the amine in a planar conformation I get one negative frequency. The energy of the pyramidal conformer is higher than that of the pyramidal one, but when I take into consideration the zero point energy correction the planar conformer (with the negative frequency) has lower energy than the pyramidal one (all positive frequencies). Does anyone have a clue as to why? Any help is appreciated. Ali From chemistry-request@server.ccl.net Wed Nov 29 09:48:19 2000 Received: from acaix1.ucis.dal.ca (acaix1.UCIS.Dal.Ca [129.173.1.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA16813 for ; Wed, 29 Nov 2000 09:48:18 -0500 Received: from is.dal.ca (wang@IS.Dal.Ca [129.173.1.52]) by acaix1.ucis.dal.ca (8.9.0/8.9.0) with ESMTP id KAA14930 for ; Wed, 29 Nov 2000 10:48:05 -0400 Received: from localhost (wang@localhost) by is.dal.ca (8.10.1/8.10.1) with SMTP id eATEm43141260 for ; Wed, 29 Nov 2000 10:48:04 -0400 Date: Wed, 29 Nov 2000 10:48:04 -0400 (AST) From: Richard Liangchen Wang To: "'chemistry@ccl.net'" Subject: database of structures and properties of molecules Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Whether someone there can kindly provide me the information on database of structures and properties of molecules, especially small molecules. Thanking you all in advance, Richard Wang From chemistry-request@server.ccl.net Wed Nov 29 11:39:42 2000 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA17191 for ; Wed, 29 Nov 2000 11:39:41 -0500 Received: from lycose.saclay.cea.fr (lycose.saclay.cea.fr [132.166.192.104]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.2.D20+Y2K) with ESMTP id RAA07576 for ; Wed, 29 Nov 2000 17:39:25 +0100 (MET) Received: from penelope.saclay.cea.fr (unverified) by lycose.saclay.cea.fr (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Wed, 29 Nov 2000 17:29:00 +0100 Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2650.21) id ; Wed, 29 Nov 2000 17:41:49 +0100 Message-ID: From: VITORGE Pierre 094605 To: "'chemistry@ccl.net'" Subject: Summary of "visualizing vibration from Gaussian98" Date: Wed, 29 Nov 2000 17:31:13 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by muguet.saclay.cea.fr id RAA07576 I downloaded the unix version of molden, and this solved my problem (see the answers below). I have problem with the PC version: it requires a X-Windows Server in which my problem is certainly originated, however since the unix version is working, I will not try further. See more details as well as aknowledgememnts: at the end of this e-mails. The question was: Hello, I am currently using Gaussian98 on Unix workstations, entering and reading data by using a PC (Intel Windows98), typically Chem3D, I can also use a Mac. As far as i know, vibrations can be visualized with GaussView or Hypechem, unfortunately I have not got these softwares: do you know a free (or noon expensive) software that can visualize vibrations from a Gaussian98 output file? Pierre Vitorge CEA Saclay DCC/DESD/SESD UMR 8587 (Universite d'Evry-CNRS-CEA) 91191 Gif sur Yvette cedex France pierre.vitorge@cea.fr phone +33 169-08-32-65, secretary: +33 169-08-32-50, fax: +33 169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre/pierre.html ___________________________________________________ the answers are ____________ MOLEN try MOLDEN, It is freely available at http://www.caos.kun.nl/~schaft/molden/molden.html http://www.caos.kun.nl/~schaft/molden/windowsnt95.html http://www.cmbi.kun.nl/~schaft/molden/molden.htmlat ftp ftp.caos.kun.nl It runs mainly on Unix machines, but the last version can also run on Windows 95/98/NT machines (however, it requires a X-Windows Server software installed to run; see the Molden page for details). As X-Server under Windows (in Unix as well, of course : try X-Win32. Easy to use and free for 2h sessions. The demo version of X-Win32 version5.0 by Starnet.Then, if you like it you can buy it. This demo will run for two hours and then will shutdown and you have to reopen it once more www.startnet.com/productinfo ___________ GOPENMOL essayer gOpenMol, il est assez bon et, de plus, gratuit: i.e: you can try gOpenMol, it is quite good and free http://www.chem.t.u-tokyo.ac.jp/appchem/labs/kitazawa/dragoe/ http://www.csc.fi/~laaksone/gopenmol/gopenmol.html ______________ MOLDRAW MOLDRAW is free, it reads GAUSSIAN output file (and many other formats) visualizing vibrations. http://www.ch.unito.it/ifm/fisica/moldraw/moldraw.html _____ JMOL jmol (a java-based visual tool) at http://www.openscience.org/jmol . _______ MOLWIN MolWin. Look in the CCL archives, as I (E. Lewars) gave info' on this program a couple years ago. _______ MOLVIB MolVib, made by Serena Software; but I don't know how much this costs. ______________ AKNOWLEDGEMENTS in the order as received: (REMERCIEMENTS dans l'ordre de reception) Wolfgang Roth, TU Brauschweig, Instit.f.Phys.Theor.Chem. Braunschweig, Germany Jesus Orduna Instit.Ciencia de Mater.Aragon, Unidad de Nuev.Mater.Orgá., Facultad de Ciencias CSIC-Univ. Zaragoza Spain N. Dragoe Dorothee Berthomieu, Lab.Mater.Catalytiques et Catalyse, Chim.Orga., CNRS, Ecole Nationale Sup.Chim. Montpellier, France Dr. Theodorus J.M. de Bruin, Univ.J.Fourier, LEDSS VII, Chim. Théorique CNRS Grenoble FRANCE Peter Dinér Ph. D. Stud., Dpt.Chem., Orga. Chem., Göteborg Univ. Sweden Jerome Golebiowski, Lab.Aromes, Syntheses & interactions, Univ.Nice - Sophia Antipolis, France ... Sergio Galembeck Stefan Manu Bruce Tattershall, Dpt. Chem. Univ. Newcastle, England Tanja van Mourik, Royal Soc. Univ., Res.Fellow Chem.Dpt., Univ.College London, England Theoretical Chemistry Group, Univ. of Torino, Italy Fabrice Leclerc, Ph.D., Lab. MAEM, CNRS-UHP Nancy, France Nicolas FERRE, Lab. Chim.Theorique, Univ. H.Poincare, Nancy, FRANCE Sofia Godinho, Ph-D stud. ITQB-UNL, Portugal Nicolas SAETTEL Univ.Notre Dame Dept.Chem.Biochem., NOTRE DAME,IN E. Lewars From chemistry-request@server.ccl.net Wed Nov 29 12:42:54 2000 Received: from correu.urv.es (correu.urv.es [193.144.16.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA17454 for ; Wed, 29 Nov 2000 12:42:51 -0500 Received: from pcqf-10 (pcqf-10.urv.es) by correu.urv.es (Sun Internet Mail Server sims.3.5.1999.05.24.18.28.p7) with SMTP id <0G4S00K1KRUSSX@correu.urv.es> for CHEMISTRY@ccl.net; Wed, 29 Nov 2000 18:42:28 +0100 (MET) Date: Wed, 29 Nov 2000 18:50:43 +0100 From: Carles Bo Jane Subject: New ADF utilities and Bader's charge density analysis software X-Sender: bo@quimica.urv.es To: adf-list@scm.com, CHEMISTRY@ccl.net Message-id: <3.0.3.32.20001129185043.0069b2ac@quimica.urv.es> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Content-type: text/plain; charset=us-ascii Dear colleagues, I'd like to draw your attention to some utilities we have written for ADF, as well as to Xaim (a GUI to perform Bader's analysis). These programs are freeware and available at: ADF utilities: http://www.quimica.urv.es/ADF_UTIL Xaim : http://www.quimica.urv.es/XAIM Best wishes, Carles ________________________________________________________________ Carles Bo Dept. de Quimica Fisica i Inorganica Universitat Rovira i Virgili Voice (34) 977 55 95 69 Pl. Imperial Tarraco, 1 FAX (34) 977 55 95 63 43005 - Tarragona SPAIN http://www.quimica.urv.es/~w3qfi http://quimica.urv.es/cgi-bin/card?bo+qfi ________________________________________________________________ From chemistry-request@server.ccl.net Wed Nov 29 18:06:03 2000 Received: from mr.usu.edu (mr.usu.edu [129.123.1.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA19047 for ; Wed, 29 Nov 2000 18:06:02 -0500 Received: from tapaskar (tapaskar.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id CF5AA1D389 for ; Wed, 29 Nov 2000 16:06:00 -0700 (MST) Message-ID: <00c201c05a58$d2e77560$25037b81@tapaskar> From: "Tapas Kar" To: Subject: Problem:AIM in G98 Date: Wed, 29 Nov 2000 16:05:10 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi, I got the following error while doing AIM calculation using G98. FATAL ERROR: TOO MANY PATCHES Error termination via Lnk1e in /app/g98A7/g98/l609.exe. What's wrong here and how to solve it. Tapas _______________________________________ Tapas Kar, Ph.D Department of Chemistry & Biochemistry Utah State University 0300 Old Main Hill Logan, UT 84322-0300 Voice: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu tapas@risky3.chem.usu.edu -----------------------------------------