From chemistry-request@server.ccl.net Thu May 17 05:31:54 2001 Received: from ns.ice.mpg.de ([195.37.47.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4H9VsI24946 for ; Thu, 17 May 2001 05:31:54 -0400 Received: from relax.ice.mpg.de ([195.37.47.207] helo=ice.mpg.de) by ns.ice.mpg.de with esmtp (Exim 3.14 #17) id 150K7o-000559-00 for chemistry@ccl.net; Thu, 17 May 2001 11:31:16 +0200 Message-ID: <3B039A88.E71014CE@ice.mpg.de> Date: Thu, 17 May 2001 11:31:52 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: Gaussian 98 in PCcluster References: <200105170635.f4H6Z0m05957@server.ccl.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Digest Mailer of CCL wrote: > >From chemistry-request@server.ccl.net Wed May 16 04:54:22 2001 > Date: Wed, 16 May 2001 11:54:19 +0300 (EEST) > From: Maija Lahtela > To: > Subject: Gaussian 98 in PCcluster > > Dear All, > > We are going to build up a PC cluster wiht Red Hat linux in order to run > Gaussian 98 A.9. Our propose is to start with 16 PCs and then enlarge it > 100 PCs. > > We have have tested by running Gaussian with one PC but the results has > not been very couraging while the code is slow. We have do not have Kinda > yet. However, I have found articles about running Gaussian with mpi which > sounds interesting for us. > > We would appreciate if you could give us hint where we could find gaussian > mpi version or how you have build up your custer to run Gaussian jobs. > > Thanks in advance! I will summarize. I'm using a 16 node PC cluster for running Gaussian 98 using Linda as the parallel execution environment. Works nicely. It must, however, be noted that for our type of calculation, a reasonable scaling is only achieved up to eight or ten nodes per job. The results of our initial, provisional evaluation are summarized under http://www/departments/ChemInf/edda.html. Follow the last link on the scaling behaviour. The result of this behaviour is that I use the OpenPBS batch queue system to load-schedule jobs between subclusters of eight nodes each. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Carl-Zeiss-Promenade 10, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Thu May 17 04:55:46 2001 Received: from mailhost1.rdg.ac.uk ([134.225.16.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4H8tgI25852 for ; Thu, 17 May 2001 04:55:44 -0400 Received: from indyp.chemistry ([134.225.168.35] helo=indyp.chemistry.rdg.ac.uk) by mailhost1.rdg.ac.uk with esmtp (University of Reading Email Service) id {150JZ7-0005C6-00} for CHEMISTRY@server.ccl.net; Thu, 17 May 2001 09:55:25 +0100 Received: from reading.ac.uk (localhost [127.0.0.1]) by indyp.chemistry.rdg.ac.uk (SGI-8.9.3/8.9.3) with ESMTP id JAA89780 for ; Thu, 17 May 2001 09:58:07 -0100 (BST) Sender: dave@reading.ac.uk Message-ID: <3B03AEBF.27DBA949@reading.ac.uk> Date: Thu, 17 May 2001 09:58:07 -0100 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: Point charges in g98- do they work? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Fellow Computational Chemists, I am trying out some stuff including point charges and, in separate calculations, the ONIOM methodology. First question- Do point charges work? I have tried as a test putting a big point charge at the end of a hydrogen molecule and see no polarisation or asymmetry. (this is using the line- charge +5.0 0.000000 0.000000 2.0 after the cartesian description of the molecule and I also tried adding a 0 before charge as it was in one of the examples.) Any help? Secondly, Is there any way of including ones own vdW parameters in the UFF part of the ONIOM implementation? And turning bonding off? Thanks in advance. Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price MA CChem MRSC Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu May 17 10:45:33 2001 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4HEjWI19349 for ; Thu, 17 May 2001 10:45:32 -0400 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id QAA24847; Thu, 17 May 2001 16:41:54 +0200 (MET DST) for Received: from vub.ac.be (algcpc3.vub.ac.be [134.184.24.93]) by mach.vub.ac.be (8.9.3/3.13.2.ap (mach)) id QAA12766; Thu, 17 May 2001 16:44:59 +0200 (MET DST) for Message-ID: <3B03E34E.DBC31A2B@vub.ac.be> Date: Thu, 17 May 2001 16:42:22 +0200 From: Pierre Mignon X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: G98 output file-density matrix Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am confused with a problem with Gaussian 98. I'd like to have the density matrix condensed to atoms in the output file. I can obtain it when I make calculation with a small number of atoms, but in the system I study, there are 100 atoms and the output doesn't contain the density matrix condensed to atoms or the inter-atomic distance matrix. I 'd like to see it. If someone can help me ... Thank's in advance. Pierre Mignon Free University of Brussel From chemistry-request@server.ccl.net Thu May 17 10:04:21 2001 Received: from ns.ice.mpg.de ([195.37.47.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4HE4LI19069 for ; Thu, 17 May 2001 10:04:21 -0400 Received: from relax.ice.mpg.de ([195.37.47.207] helo=ice.mpg.de) by ns.ice.mpg.de with esmtp (Exim 3.14 #17) id 150ONS-0002Dd-00; Thu, 17 May 2001 16:03:42 +0200 Message-ID: <3B03DA62.A7E00238@ice.mpg.de> Date: Thu, 17 May 2001 16:04:18 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Richard Walsh , ccl Subject: Re: CCL:Gaussian 98 in PCcluster References: <200105171358.IAA22239@us.msp.networkcs.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Richard Walsh wrote: > > Dr. Steinbeck, > > The website suggested seems to be non-functional: > > http://www/departments/ChemInf/edda.html For obvious reasons :-) I apologize for the inconvenience. The correct URL of course is: http://www.ice.mpg.de/departments/ChemInf/edda.html Regards, Christoph Steinbeck -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Carl-Zeiss-Promenade 10, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Thu May 17 12:05:36 2001 Received: from mail.takas.lt ([212.59.0.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4HG5ZI20179 for ; Thu, 17 May 2001 12:05:36 -0400 Received: from julius (dialup492.vln.takas.lt [212.59.29.196]) by mail.takas.lt (8.9.1/8.9.0) with SMTP id SAA1882720 for ; Thu, 17 May 2001 18:05:29 +0200 (GMT+0200) Message-ID: <00a601c0deea$daf867c0$c41d3bd4@ktl.mii.lt.lorka.ktl.mii.lt> From: "Olegas Eicher-Lorka" To: Subject: G98W on Dual processors Date: Thu, 17 May 2001 17:36:29 +0200 Dear CClers, We've been using G98W for about a year on a lowly PC. We're just about = to get a dual processor system (2*PIII 933MHz) and were looking forward = to fast calcuations only to be told that G98W only runs on a single = processor. Any add-ons, tips or advice? Thanks Dr. Olegas Eicher-Lorka Institute of Chemistry Akademijos 7 e-mail: lorka@takas.lt tel.: +(370-)2-729372 From chemistry-request@server.ccl.net Thu May 17 13:25:08 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4HHP8I20957 for ; Thu, 17 May 2001 13:25:08 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id TAA09333 ; Thu, 17 May 2001 19:25:02 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id TAA28334; Thu, 17 May 2001 19:24:36 +0200 Date: Thu, 17 May 2001 19:24:36 +0200 Message-Id: <200105171724.TAA28334@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: mike_smith07@yahoo.com CC: CHEMISTRY@ccl.net In-reply-to: <20010516225652.94948.qmail@web13206.mail.yahoo.com> (message from mike smith on Wed, 16 May 2001 15:56:52 -0700 (PDT)) Subject: Re: CCL:Confusion on ensemble average for biomolecule References: <20010516225652.94948.qmail@web13206.mail.yahoo.com> > THEORETICALLY, should we do sampling of initial > velocities for a large number of trajectories to let > the STATISTICAL MECHANICS make sense? However, in > reality, it's impratical to do that. Usually one assumes that the system is ergodic, i.e. reaches any point in phase space if one waits long enough. Then a time average over a single trajectory is equal to an ensemble average over many trajectories with different initial conditions. Unfortunately, real MD trajectories for macromolecular systems are never long enough to assume sufficient sampling of all coordinates. Usually they are even too short by at least an order of magnitude. One attempt to overcome this is to run several trajectories from different initial conditions that are reasonably independent - that means not only different velocities, but also different initial configurations. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu May 17 13:45:28 2001 Received: from wally.uh.cu ([216.72.24.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4HHisI21055 for ; Thu, 17 May 2001 13:45:25 -0400 Received: from alma.uh.cu (alma.uh.cu [192.168.100.67]) by wally.uh.cu (8.11.0/8.11.0/MZ) with ESMTP id f4HHoRO02981; Thu, 17 May 2001 13:50:27 -0400 Received: from ffserver.ff.oc.uh.cu (ff.oc.uh.cu [192.168.100.83]) by alma.uh.cu (Postfix) with ESMTP id 2479DA5611; Thu, 17 May 2001 13:48:52 -0400 (CDT) Received: from ffuh.ff.oc.uh.cu (IDENT:root@ffuh.ff.oc.uh.cu [192.168.11.1] (may be forged)) by ffserver.ff.oc.uh.cu (8.9.3/8.9.3/JP) with ESMTP id IAA00985; Thu, 17 May 2001 08:59:11 -0400 Received: from raman.ff.oc.uh.cu (IDENT:eariel@raman.ff.oc.uh.cu [192.168.11.201]) by ffuh.ff.oc.uh.cu (8.9.3/8.9.3/JP) with ESMTP id NAA10221; Thu, 17 May 2001 13:15:51 -0400 Received: from localhost (eariel@localhost) by raman.ff.oc.uh.cu (8.8.7/8.8.7/JP) with SMTP id OAA13200; Thu, 17 May 2001 14:11:52 -0400 Date: Thu, 17 May 2001 14:11:52 -0400 (EDT) From: "Eduardo A. Menendez Proupin" To: Olegas Eicher-Lorka Cc: chemistry@ccl.net Subject: Re: CCL:G98W on Dual processors In-Reply-To: <00a601c0deea$daf867c0$c41d3bd4@ktl.mii.lt.lorka.ktl.mii.lt> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Please, summarize the answers and send me- Regards Eduardo On Thu, 17 May 2001, Olegas Eicher-Lorka wrote: > > Dear CClers, > We've been using G98W for about a year on a lowly PC. We're just about = > to get a dual processor system (2*PIII 933MHz) and were looking forward = > to fast calcuations only to be told that G98W only runs on a single = > processor. > > Any add-ons, tips or advice? > > Thanks > > Dr. Olegas Eicher-Lorka > Institute of Chemistry > Akademijos 7 > e-mail: lorka@takas.lt > tel.: +(370-)2-729372 > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > Eduardo Ariel Menendez Proupin, Ph.D. ------------------------------------- Laboratorio de Ingenieria de Zeolitas Instituto de Materiales y Reactivos Universidad de La Habana San Lazaro y L. Vedado 10400 La Habana, Cuba E-mail:eariel@raman.ff.oc.uh.cu Fax : (53+7)+320018/794651 Phone: (53+7)+788950/788956/788957 ext 553 (53+7)+707666/705707 From chemistry-request@server.ccl.net Thu May 17 14:10:52 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4HIAqI21211 for ; Thu, 17 May 2001 14:10:52 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id OAA23105; Thu, 17 May 2001 14:10:52 -0400 (EDT) Date: Thu, 17 May 2001 14:10:51 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: From the maintainer of CCL Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Subscriber, This is your list maintainer speaking {:-)}... Do not touch this d(ial)... I will try to be short... This will consist of: help-mes, my plans, thank yous, and appeal to your benevolent instincts (i.e., help guys and galls, again...). I want to thank all of you who either bought CCL Archives CD sets from us, or who gave us donations. Your help is very needed and VERY APPRECIATED. All the CCL members owe you for that, since this keeps CCL running. If you did not do it yet, please help CCL financially: You can either get invoiced and buy set of 4 CDs representing CCL Archives, or just give us a donation which can be deducted from taxes in the US, and probably other countries too. For details check: http://www.ccl.net/chemistry/aboutccl/supporting/ Again I want to thank all of you who helped me up to date. No donation is too small, and if each of you gave me $25 I would have all my needs covered. But since the current number of supporters is less than a hundred, please try also to make up for those who cannot or may not contribute. We will soon have vacation time. For some of us it is the busiest time to do research, since the lines to equipment are shorter, many students are gone fishing, and the teaching load is low... For some of us it is time we do travel, take a rest, go to conferences, etc. I will take some time off during summer, early June to mid July (guess where I go: to Poland... and hopefully to some other countries around). While usually I want to be close to a phone jack and have a laptop at hand, this time may be different. I plan to spend some time out there in the middle of nowhere (namely on the ridges of Beskid mountains). At the same time, I want the CCL to continue operating... The only way CCL can continue operation is that I get help. Thanks to the OSC management and their help and encouragement, and the help of CCL subscribers through their donations and purchases, I have some hourly/undergraduate students working with me in maintaining CCL and doing the daily chores. This is tremendous help since I am getting busier and busier every month (or maybe I just get less efficient {:-)}) and without the help of students, it would be very hard for me to keep CCL going. Unfortunately, the student turnaround is quite fast, and once they learn "the stuff" about Web and sysadm, they get better jobs outside OSU campus. I would like to have a more stable environment for CCL and more experienced students to operate the resource. It would be nice to have it now, before I take off abroad. One way of achieving it is to get Graduate Student Assistants (GRA) who are more dependable, more experienced, and if you pay their tuition, they have a reason to stay with you. Vacations is also good time to get the students since it is decision time for them. CCL has a lot of needs: update archives, find new material, install and improve operating software for the list and Web site, upgrade hardware and organization, upgrade firewall and security, etc... Please consider helping me financially. Now you can use research grant money to do this. Review the page: http://www.ccl.net/chemistry/aboutccl/supporting/ If you are a graduate student, please encourage your Ph.D. advisor to buy the CCL Archives CD Set. Just do it, please... If you cannot help financially, please consider contributing good messages to CCL discussions, and give us some software or write-ups to put in CCL archives. Please help me in keeping this resource useful, current, and interactive. Note that we also want to expand our service to the community with more specialized discussions lists: http://www.AtomicScaleDesign.Net We are operating within the academic environment and we are very careful to have a broad support base and non-allied status. In is not about money for us, and if we cannot do it this way, we will not do it. Please help!!! Thank you for you attention and contributions throughout all these years. Can you imagine that the CCL is more than 10 years old? We were here before the Web and hype... So please help us to be here now and long after the scum and hype dissipates. Jan Labanowski jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Thu May 17 16:58:09 2001 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4HKvpI22331 for ; Thu, 17 May 2001 16:57:54 -0400 Received: from lauca.usach.cl ([158.170.51.105]) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id f4HKtDW13598 for ; Thu, 17 May 2001 16:55:13 -0400 (CST) Message-ID: <3B043B99.D7D3B356@lauca.usach.cl> Date: Thu, 17 May 2001 16:59:05 -0400 From: Danilo Gonzalez X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: ComFA for linux.. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all! Anybody know a version of ComFA for linux?... or other system (QSAR) similar to ComFA for linux or windows? I will summarize the answers,...thanks a lot! Danilo Gonzalez. Faculty of Chemistry and Biology University of Santiago of Chile.