From morokuma@euch4e.chem.emory.edu Thu Feb 6 09:21:21 1997 Received: from euch4e.chem.emory.edu for morokuma@euch4e.chem.emory.edu by www.ccl.net (8.8.3/950822.1) id IAA29850; Thu, 6 Feb 1997 08:42:05 -0500 (EST) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA22551; Thu, 6 Feb 1997 08:19:25 -0500 Message-Id: <9702061319.AA22551@euch4e.chem.emory.edu> Subject: Emory University Visiting Fellowship Program To: chemistry@www.ccl.net Date: Thu, 6 Feb 1997 08:19:24 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Cheery L. Emerson Center for Scientific Computation VIsiting Fellowship Program at Emroy University The Cherry L. Emerson Center for Scientific Computation (Director: Keiji Morokuma) offers Visiting Fellowships for long-term (3-12 months) and short-term (1-3 months) visitors on computational chemistry and physics. It provides stipend or partial support for long-term visiting fellows on leave or sabbatical from their permanent jobs and travel expenses for short-term visiting fellows.i (This is not a postdoctoral fellowship.) The deadline for the application this year is March 1, 1997. For details, visit the web site: http://www.emerson.emory.edu/fellows/fellers.html and contact morokuma@emory.edu. ______________________ Keiji Morokuma Emerson Center for Scientific Computation and Department of Chemistry Emory University Atwood Hall, 1515 Pierce Dr., Atlanta, GA 30322, USA Phone (404) 727-2180; Fax (404) 727-6586 E-mail: morokuma@emory.edu From ccl@www.ccl.net Fri Feb 7 04:21:33 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id DAA07864; Fri, 7 Feb 1997 03:52:54 -0500 (EST) Received: from cit.enscm.fr for gabriele@palladium.enscm.fr by bedrock.ccl.net (8.8.3/950822.1) id DAA00650; Fri, 7 Feb 1997 03:52:51 -0500 (EST) Received: from palladium.enscm.fr by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA15218; Fri, 7 Feb 1997 09:49:35 +0100 Received: from palladium (localhost [127.0.0.1]) by palladium.enscm.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA20856 for ; Fri, 7 Feb 1997 09:58:29 +0100 Sender: gabriele@palladium.enscm.fr Message-Id: <32FAEEB5.41C6@palladium.enscm.fr> Date: Fri, 07 Feb 1997 09:58:29 +0100 From: Gabriele VALERIO Organization: Ecole Nationale Superieure de Chimie de Montpellier X-Mailer: Mozilla 3.0Gold (X11; I; IRIX64 6.2 IP21) Mime-Version: 1.0 To: chemistry@ccl.net Subject: palladium basis set Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, I am looking for an extended gaussian basis set for Pd. Any hint? I already checked the EMSL GAUSSIAN BASIS SET repository, but unfortunately with no success. Thank you in advance for the help you will surely provide. Best Regards, Gabriele -- Dr. Gabriele VALERIO Laboratoire de Materiaux Catalytiques et Catalyse en Chimie Organique UMR 5618 ENSCM-CNRS Ecole Nationale Superieure de Chimie Tel: 33-4-67144396 8, rue de l'Ecole Normale Fax: 33-4-67144349 34296 Montpellier cedex 5 (FRANCE) mailto:gabriele@palladium.enscm.fr From Lchen@mdli.com Fri Feb 7 12:21:35 1997 Received: from mdli.com for Lchen@mdli.com by www.ccl.net (8.8.3/950822.1) id MAA10983; Fri, 7 Feb 1997 12:10:44 -0500 (EST) Received: from puffin.mdli.com ([191.254.19.10]) by mdlgate.mdli.com with ESMTP id <17637>; Fri, 7 Feb 1997 08:51:31 -0800 Received: from gimli.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id RAA03756; Fri, 7 Feb 1997 17:09:02 GMT Received: from Trumpetfish.mdli.com by mdli.com (PMDF V5.1-5 #15780) with SMTP id <01IF4NRGV8UGHT2YZ7@mdli.com> for chemistry@www.ccl.net; Fri, 7 Feb 1997 09:09:56 PST Date: Fri, 7 Feb 1997 09:07:45 -0800 From: Lingran Chen Subject: SUMMARY: Chemical Programs for Linux To: chemistry@www.ccl.net Reply-to: Lchen@mdli.com Message-id: <32FB6161.722E@mdli.com> Organization: MDL Information Systems, Inc. MIME-version: 1.0 X-Mailer: Mozilla 3.01Gold (Win95; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hi CCL friends: About two weeks ago I posted here the following question: > In the past years I used Pentium PC/Linux as a main platform > for developing the SYNGEN system > (http://syngen2.chem.brandeis.edu/syngen.html) and for Web Server. > I found this PC workstation is just fine. > > And I would like to know how many chemical programs have been ported > to or developed on Linux and/or how many chemists are using Linux. > Any information on this question will welcome and I will summarize > the responses. Thanks. Thanks a lot for all the responses which are summarized below, as promised. However, before offering the summary, I would like to show you some ====================================================== Interesting Web Sites on LINUX ====================================================== What is Linux? - http://www.ssc.com/linux-int/Introduction/linux.html What can Linux do? - http://www.ssc.com/linux-int/Introduction/capabilities.html How many machines have run Linux ? - http://www.ssc.com/linux-int/News/Linux/v2.0/PR-Linux.2.0.0-English.html Where to find other scientific applications on Linux ? - http://www.KachinaTech.COM/SAL/ Is Linux as easy to use as Mac OS ? - http://www.ssc.com/linux-int/News/linux-pro.html Is Linux more reliable than commercial UNIX ? - http://www.ssc.com/linux-int/Introduction/Usenet/case6.html Where to obtain Linux ? - http://www.ssc.com/linux-int/Introduction/where.html ====================================================== SUMMARY: Chemical Programs for Linux ====================================================== From: Wolf-Dietrich Ihlenfeldt Wir haben eine Reihe von Programmen auf Linux laufen, unter anderem die ganzen CACTVS Tools. (Please check: http://schiele.organik.uni-erlangen.de/ -Lingran) --------------------------------------------------------------------------------------------- From: Bryan Van Vliet I have a Linux machine in my home office. I put it together with a Pentium motherboard clone and parts from old computers. It is very fast and nice. It serves as my firewall/mail server/web server machine. I am using Slackware Linux. --------------------------------------------------------------------------------------------- From: Marcus G Martin We have recently started using a PC with Linux for running our in house Gibbs Ensemble - Configurational Bias Monte Carlo code. We determine phase diagrams, among other things, and a single run typically takes a week or two of cpu time. We found it was quite easy to port our code (written in fortran) to the Linux system and also get great speed from our 200 MHz Pentium Pro. --------------------------------------------------------------------------------------------- From: Bill Ross ross@cgl.ucsf.EDU People have been running AMBER on linux. See the benchmarks on our web page for comparison w/ other machines (I'm about to add PPro numbers). (check: http://www.amber.ucsf.edu/amber/) --------------------------------------------------------------------------------------------- From: Satyam Priyadarshy Our department have a large number of SGI workstations and Dec Alpha workstations. Within last couple of months we have acquired a couple of Pentium Pro (single and dual processor) and we are running them with Linux.. The Pro's are faster for quantum calculations cf. R8000 of SGI using Gaussian. We are hoping that the use of Linux will grow in this Department with time and more and more chemistry related software will be available. --------------------------------------------------------------------------------------------- From: Jan Reimers I am more of a materials scientist with a PhD degree in chemistry. I use a Linux/PC system as an inexpensive scientific workstation for Monte Carlo simulations and electronic structure calculations. I also find Linux be an excellent environment for software development. I am currently developing a DFT program for dealing with solids containing d and f elements. The program is designed to use a wide variety of basis functions AO's, Gaussians, contracted gaussians, plane waves, etc. I have chosen to use C++ for this project in order to manage the complexity of the task. Using an OO programming approach allows one to abstract away the details of the various basis functions, so that most of the code has no notion of precise nature of the basis function it is dealing with. Linux just happens to come with a C++ compiler (g++-2.7.2), and the multitasking allows me to do other work while long compilations are going. I currently just pipe (unix pipe concept) data into gnuplot for plotting. I have not yet investigated any of the more elaborate visualization tools that are available. I intend to try ViewMol if a statically linked version becomes available. I am very pleased that I can carry out my sort of project at home without having make a large initial monetary investment in software (real OS, good compiler, editor, revision control, plotting, etc.) to get going. Only 5 years ago this would have been a very expensive project just to get started on, in terms of OS and development tools. It is quite possible that I would benifit from a commercial C++ compiler, but at the moment g++ is adequite, and it also gaurantees portability to a very wide variety of platforms. --------------------------------------------------------------------------------------------- From: Dr. Ir. David van der Spoel spoel@rugmd17.mdli.com The GROMACS Molecular Dynamics code runs under linux http://rugmd0.chem.rug.nl/~gmx Performance on a 133 MHz pentium is comparable to an SGI Indy workstation (MIPS R4600) --------------------------------------------------------------------------------------------- From: Ezequiel Quintana Morales I use Linux each time that I can. I run Mopac (caculations), Gifa (NMR), RasMol (viewer), Babel (change bewten file formats). I think that Linux has a big future ahead. --------------------------------------------------------------------------------------------- From: "Edward S. Blurock" I am currently porting the REACTION, a system for modeling complex reaction systems such as combustion mechanisms, to Linux. It is a C++ application with a JAVA interface. For more info about REACTION itself see http://info.risc.uni-linz.ac.at:/people/blurock/REACTION/toppage.html --------------------------------------------------------------------------------------------- From: Carles Bo bo@argo.urv.es (Carles Bo) We are porting ADF to Linux. check the http://tc.chem.vu.nl/SCM/Welcome.html to get more information about ADF. --------------------------------------------------------------------------------------------- From: "Dr. Teerakiat Kerdcharoen" I also used LINUX/Pentium for production runs of my research in molecular dynamics simulations. Most of the time, I used in-house developed codes and sometime public domain source codes from Daresbury Laboratory library of molecular dynamics softwares in UK, http://www.dl.ac.uk/CCP/CCP5/main.html Most of the codes there are written in FORTRAN and certainly portable to LINUX. I would also suggest a Homepage of collection of LINUX's scientific software at, http://www.KachinaTech.COM/SAL/ --------------------------------------------------------------------------------------------- From: "Dr.Larissa Steinhauer" Auf meiner Seite: http://schiele.organik.uni-erlangen.de/Valentin_Steinhauer findest Du viele Anwendungen for LINUX und JAVA. --------------------------------------------------------------------------------------------- From: Margaret Wong We do quite a bit of visualisation, analysis of data and run a web server from our linux box. Nearly anything written in C (with xwindows graphics) can be run easily. --------------------------------------------------------------------------------------------- From: Pedro A M Vazquez We're using FreeBSD (www.freebsd.org) instead of linux but I believe most of programs were ported to both as both use the same programing tools: gcc/f2c gnu g77 sun libm xfree86 mesa motif opengl etc To my knowledge the following programs are running in both systems for at least a year gamess (even the parallel version) gaussian94 mopac (6,7,93) molview molden rasmol mm2 mm3 and many more I can't recall now, these are the most used at my site. I can't remember a fortran or C program with available source code that was unportable to one or another being portable to a mainstream Unix brand. As far as I know the only big diference between Linux and FreeBSD is the file size limitation on Linux (2.0G, and presumed to be removed soon) and slightly different behaviours of libm among different distributions (Slackware, RedHat, etc) . --------------------------------------------------------------------------------------------- Thanks. -Lingran ********************************************************** Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. 14600 Catalina Street San Leandro CA 94577 Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM URL: http://www.mdli.com http://syngen2.chem.brandeis.edu/~chen/lingran.html ********************************************************** From XIENING@MEENA.CC.UREGINA.CA Sat Feb 8 03:21:45 1997 Received: from veena.cc.uregina.ca for XIENING@MEENA.CC.UREGINA.CA by www.ccl.net (8.8.3/950822.1) id DAA26758; Sat, 8 Feb 1997 03:17:01 -0500 (EST) Received: from meena.cc.uregina.ca by meena.cc.uregina.ca (PMDF V5.1-6 #20153) id <01IF5NMHQ1XM9PMGAH@meena.cc.uregina.ca> for chemistry@www.ccl.net; Sat, 8 Feb 1997 02:16:42 CST Date: Sat, 08 Feb 1997 02:16:42 -0600 (CST) From: Ning Xie Subject: MnO4- & ZnCl2 complex To: chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Hi, there, I need to calculate the HOMO/LUMO energies and the heat of formation of MnO4-, ZnCl2 (or other lewis acid) and the complex of them i.e [MnO4 ZnCl2]. Especially for the complex, I don't have any experimental or calculated data of its structure. Is there anybody who can give me some suggestions? Thank you in advance. ========================================================================= | XIE, NING Tel: (306)585-5262 (O) | | Chemistry Department (306)585-2184 (H) | | University of Regina E-Mail: xiening@meena.cc.uregina.ca | | Regina, SK or: xiening2@max.cc.uregina.ca | | Canada S4S 0A2 | ========================================================================= From sakul@chem.unipune.ernet.in Sat Feb 8 08:21:50 1997 Received: from sangam.ncst.ernet.in for sakul@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id IAA27401; Sat, 8 Feb 1997 08:10:39 -0500 (EST) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id SAA16764 for ; Sat, 8 Feb 1997 18:46:19 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA18080; Sat, 8 Feb 1997 18:38:55 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (5.0/SMI-SVR4.1.0) id AA18441; Sat, 8 Feb 1997 18:40:10 +0500 Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id TAA02724; Sat, 8 Feb 1997 19:41:43 -0500 Date: Sat, 8 Feb 1997 19:41:43 -0500 From: sakul@chem.unipune.ernet.in (Dr. Sudhir Kulkarni) Message-Id: <199702090041.TAA02724@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Cation binding to neutral molecules Dear Sirs: I am interested in the complexes of cation-neutral molecule. I shall be grateful to you if you can send me the references of recent works on 'CATION BINDING' studied experimentally or theoretically. Thank you very much. Subhash S. Pingale e-mail : gadre@parcom.ernet.in e-mail : gadre@chem.unipune.ernet.in e-mail : sakul@chem.unipune.ernet.in ************************************************************************* From maiden@RedBrick.DCU.IE Sat Feb 8 08:44:20 1997 Received: from tolka.dcu.ie for maiden@RedBrick.DCU.IE by www.ccl.net (8.8.3/950822.1) id HAA27306; Sat, 8 Feb 1997 07:45:17 -0500 (EST) Received: from Nurse.RedBrick.DCU.IE by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA10840; Sat, 8 Feb 1997 12:45:16 GMT Received: (from maiden@localhost) by RedBrick.DCU.IE (SomeMTA) id MAA28884; Sat, 8 Feb 1997 12:44:05 GMT Organisation: DCU Networking Society X-Disclaimer: The DCUNS is not responsible for the content of this message Date: Sat, 8 Feb 1997 12:44:05 +0000 (GMT) From: "Mick the imp (not my account!)" To: CHEMISTRY@www.ccl.net Subject: query.... Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCL. I am probably out of my depth here, but i have to ask three questions 1: Can someone please DEFINE BSSE...I see it all the time and i have a reasonable idea, but i do not know how to define it. It is important that i do for my final year research project. 2: How do I "explore transition states / reaction pathways" using Gaussian and/or Gamess_UK. 3: Is Gamess_UK good for DFT calculations? Thank you Michael Nolan CG4 - chemistry + German, year 4. Dublin City University Glasnevin Dublin 9 Ireland "what is a man that an electron is mindful of him" From badertscher@org.chem.ethz.ch Sat Feb 8 13:21:48 1997 Received: from org.chem.ethz.ch for badertscher@org.chem.ethz.ch by www.ccl.net (8.8.3/950822.1) id MAA28415; Sat, 8 Feb 1997 12:44:22 -0500 (EST) Received: from [129.132.67.36] (chn-c63d.ethz.ch [129.132.67.36]) by org.chem.ethz.ch (940816.SGI.8.6.9/8.6.10) with SMTP id SAA03248 for ; Sat, 8 Feb 1997 18:46:27 +0100 X-Sender: badertscher@aida.ethz.ch Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 8 Feb 1997 18:45:12 +0100 To: chemistry@www.ccl.net From: badertscher@org.chem.ethz.ch (Martin Badertscher) Subject: interaction: cation - neutral molecules Most efficient: one answer to two requests: 1. Subhash S. Pingale wrote: > I am interested in the complexes of cation-neutral molecule. I shall > be grateful to you if you can send me the references of recent works > on 'CATION BINDING' studied experimentally or theoretically. This is the topic of my dissertation, and I am still interested in the field. I have not published recently, but I am still monitoring the field. I have plenty of unpublished results and I believe I can help you if you have particular questions. ====== 2. Michael Nolan wrote > 1: Can someone please DEFINE BSSE...I see it all the time and i have a > reasonable idea, but i do not know how to define it. It is important that > i do for my final year research project. I wrote a small review some time ago to explain certain particularities and pitfalls of interaction energy calculations. There I addressed the problem of the basis set superposition error, amongst other things. The separata were immediately sold out, so the paper was obviously considered relevant: Badertscher, M., et al., "Combined Application of Pair Potentials and the MM2 Force Field for the Modeling of Ionophores", Journal of Computational Chemistry, Vol 11, (1990), Nr. 7, p. 819-828 ====== If you are working in the field of modeling ionophores, or more general the interaction between cations and neutral ligands, please let me know. Provided you don't ask me how I am, how my grandmother is, and what the weather is on the campus, you may find a collaborator. Martin Badertscher, head of radiochemistry, dpt. of organic chemistry, federal institute of technology, Zurich, Switzerland E-Mail: badertscher@org.chem.ethz.ch