From chemistry-request@server.ccl.net Wed Mar 7 00:20:27 2001 Received: from iisc.ernet.in (iisc.ernet.in [144.16.64.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f275KOw24047 for ; Wed, 7 Mar 2001 00:20:25 -0500 Received: from helix.orgchem.iisc.ernet.in (IDENT:srb@orgchem.iisc.ernet.in [144.16.77.3]) by iisc.ernet.in (8.9.2/8.9.0) with ESMTP id KAA75346 for ; Wed, 7 Mar 2001 10:55:52 +0530 (IST) Received: from localhost (srb@localhost) by helix.orgchem.iisc.ernet.in (8.8.7/8.8.7) with ESMTP id KAA12717 for ; Wed, 7 Mar 2001 10:58:23 +0530 Date: Wed, 7 Mar 2001 10:58:23 +0530 (IST) From: "R.B.Sunoj" To: chemistry@ccl.net Subject: Shallow minimum Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, If there is a possibility of two minima on the PES which lie close to each other and one of them is very shallow, how one can find this shallow minimum?. In Gaussian scf=(tight,qc) will be of help? Thanks in advance, Sunoj From chemistry-request@server.ccl.net Wed Mar 7 08:28:24 2001 Received: from mail.iitk.ac.in ([210.212.54.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27DSKw27055 for ; Wed, 7 Mar 2001 08:28:21 -0500 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.2/8.9.2) with ESMTP id TAA20159 for ; Wed, 7 Mar 2001 19:02:21 +0530 (IST) Received: from [172.31.76.193] (IDENT:guest@[172.31.76.193]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with ESMTP id SAA11015 for ; Wed, 7 Mar 2001 18:48:45 +0530 (IST) Date: Wed, 7 Mar 2001 18:55:42 +0530 (IST) From: guest X-Sender: guest@localhost.localdomain To: chemistry@ccl.net Subject: repesenting trans metals in z matrix Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am a new user of gaussian. I am facing a problem in representing transision metals like molybdenum in the Z martix.I tried to represent the atom using the std atomic symbol : Mo but The execution terminates saying: Unknown centre Mo Thanks in advance. Chinmoy Ranjan From chemistry-request@server.ccl.net Wed Mar 7 00:49:49 2001 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f275nhw24210 for ; Wed, 7 Mar 2001 00:49:44 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id LAA08054 for ; Wed, 7 Mar 2001 11:17:46 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id LAA08044 for ; Wed, 7 Mar 2001 11:04:53 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Wed, 7 Mar 2001 11:04:52 +0530 (IST) From: Rajarshi Guha X-X-Sender: To: CompuChem List Subject: Energy minimizations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, could anybody advise the feasibility of doing an energy minimization ofa dinucleotide on Gaussian? Also what free/GPL'ed tools are available for docking? TIA, ------------------------------------------------------------------------ Rajarshi Guha | I am two fools, I know, for loving, Dept Of Chemistry, | and for saying so. IIT Kharagpur. | | -- John Donne email: rajarshi@presidency.com | web : www.psynet.net/jijog | ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Mar 7 05:47:49 2001 Received: from fecit-gate.fecit.co.uk (firewall-user@[193.119.134.250]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f27Almw25629 for ; Wed, 7 Mar 2001 05:47:48 -0500 Received: by fecit-gate.fecit.co.uk; id KAA11221; Wed, 7 Mar 2001 10:51:09 GMT Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma011219; Wed, 7 Mar 01 10:50:44 GMT Received: from fecit.co.uk (NT11.fecit.co.uk [192.168.101.116]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id KAA15693; Wed, 7 Mar 2001 10:34:19 GMT Message-ID: <3AA61053.4C68CCC3@fecit.co.uk> Date: Wed, 07 Mar 2001 10:41:23 +0000 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "R.B.Sunoj" CC: chemistry@ccl.net Subject: Re: CCL:Shallow minimum References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > If there is a possibility of two minima on the PES which lie close to each > other and one of them is very shallow, how one can find this shallow > minimum?. Generally, if you want to stay in a metastable minimum with low barrier: - Make sure you start close to the minimum you're searching. - If at all possible, get a good starting Hessian. If you use a lower level of theory for this, make sure that the minimum exists on this level. - Restrict the step size. > In Gaussian scf=(tight,qc) will be of help? > You might have to make it tight. The convergence method (qc or otherwise) shouldn't matter (as long as it converges at all). HTH, Herbert -- ****************************************************** * Herbert Fruchtl Tel.: +44-(0)20-8606-4650 * * FECIT Fax: +44-(0)20-8606-4422 * * 2 Longwalk Road email: fruechtl@fecit.co.uk * * Stockley Park * * Uxbridge UB11 1AB, United Kingdom * ****************************************************** From chemistry-request@server.ccl.net Wed Mar 7 09:54:55 2001 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27Estw27804 for ; Wed, 7 Mar 2001 09:54:55 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/IUPUIPO.20010306) with SMTP id JAA09235 for ; Wed, 7 Mar 2001 09:54:57 -0500 (EST) Message-ID: Date: 7 Mar 2001 09:56:29 -0500 From: "Boyd" Subject: Emerging Technologies/COMP 2001 To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear Computational Chemists, The ACS Computers in Chemistry Division (COMP) will hold its second annual symposium on emerging technologies at the ACS National Meeting, Chicago, Illinois, USA, August 26-30, 2001. Abstracts have started arriving for the "Symposium on Emerging Computational Technologies at the 125th Anniversary of the American Chemical Society". A $1000 prize, generously sponsored by Schrodinger, Inc., will be to be presented for the best talk at the symposium. You are invited to participate. The talks will be evaluated by a Panel of Experts based on the impact the research will have on the future of computational chemistry and allied sciences. The symposium will be ideal for presenting your latest and best methodological advances. To participate, e-mail a 1000-word (text-only) abstract to me no later than April 9, 2001. The talks must be original and not be repeats of talks at other ACS symposia. Sincerely, Don Donald B. Boyd, Ph.D. Organizer, COMP's Symposium on Emerging Technologies Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (for the ACS COMP division) http://chem.iupui.edu/rcc/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu COMP http://membership.acs.org/C/COMP/ Schrodinger, Inc. http://www.schroedinger.com/ From chemistry-request@server.ccl.net Wed Mar 7 11:03:51 2001 Received: from mailhub.appstate.edu (mailhub.appstate.edu [152.10.1.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27G3pw28239 for ; Wed, 7 Mar 2001 11:03:51 -0500 Received: from ws3.appstate.edu (SYSTEM@ws3.appstate.edu [152.10.1.42]) by mailhub.appstate.edu (8.11.0/8.10.1) with ESMTP id f27FxST04229 for ; Wed, 7 Mar 2001 10:59:28 -0500 Received: from CONVERSION-DAEMON.appstate.edu by appstate.edu (PMDF V6.0-24 #41615) id <01K0WVNX21PCAXBIZX@appstate.edu> for chemistry@ccl.net; Wed, 07 Mar 2001 11:03:50 -0400 (EDT) Received: from kohn.appstate.edu ("port 2339"@cohn.chem.appstate.edu [152.10.25.95]) by appstate.edu (PMDF V6.0-24 #41615) with ESMTP id <01K0WVNWJDMCAL8BBX@appstate.edu> for chemistry@ccl.net; Wed, 07 Mar 2001 11:03:47 -0400 (EDT) Date: Wed, 07 Mar 2001 11:03:38 -0500 From: Steve Williams Subject: Re: CCL:repesenting trans metals in z matrix In-reply-to: X-Sender: willsd@pop.appstate.edu To: chemistry@ccl.net Message-id: <5.0.2.1.0.20010307110007.0905ea20@pop.appstate.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Content-type: text/plain; charset=us-ascii; format=flowed At 06:55 PM 3/7/2001 +0530, guest wrote: >Dear CCLers, > I am a new user of gaussian. I am facing a problem in representing >transision metals like molybdenum in the Z martix.I tried to represent the >atom using the std atomic symbol : Mo > but The execution >terminates saying: Unknown centre Mo > Thanks in advance. >Chinmoy Ranjan Since an offline reply failed (no such user as guest@iitk.ac.in), I'll reply to the list. There is nothing inherently wrong with Mo in a gaussian Z matrix. The problem must lie elsewhere in the input file. Why don't you include the entire input file and someone (if not me) will be able to find the error(s). Steve From chemistry-request@server.ccl.net Wed Mar 7 11:01:10 2001 Received: from blackadder.cis.McMaster.CA (blackadder.CIS.McMaster.CA [130.113.128.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27G19w28207 for ; Wed, 7 Mar 2001 11:01:09 -0500 Received: from mcmaster.ca (joule.Chemistry.McMaster.CA [130.113.108.215]) by blackadder.cis.McMaster.CA with ESMTP id LAA03168 for ; Wed, 7 Mar 2001 11:01:10 -0500 (EST) Sender: jenkins@blackadder.cis.McMaster.CA Message-ID: <3AA66AEB.64D6232A@mcmaster.ca> Date: Wed, 07 Mar 2001 12:07:55 -0500 From: Samantha Jenkins Organization: McMaster University X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: SUMMARY: CCL:Basis sets for solid SiO and GeO X-Priority: 1 (Highest) References: <3AA3CBBB.4AFB108F@mcmaster.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Samantha Jenkins wrote: > > -- Dear CCL users, > > Can you advise me as to suitable basis sets to use for solid > (crystalline) SiO and GeO (NB not SiO2 or GeO2) for comparative analysis > with the CRYSTAL98 code. > > I will summarise replies, > Hi Samantha the starting point should be the CRYSTAL web site at http://www.cse.clrc.ac.uk/Activity/crystal There is an Si basis set there used in SiO2. You will then need to reoptimise the outer shells of the basis set for use in SiO. There is a discussion of this in section 4 of the manual. If you optimise a basis set for the material could you please send me a copy for inclusion on the crystal web pages. Many thanks Adrian Wander Dear Samantha > There is an Si basis set there used in SiO2. You will then > need to reoptimise the outer shells of the basis set for use > in SiO. There is a discussion of this in section 4 of the > manual. I was hoping to aviod having to do this > If you optimise a basis set for the material > could you please send me a copy for inclusion on the > crystal web pages. OK, Best wishes, Samantha Jenkins Prof. Bernard SILVI Laboratoire de Chimie Theorique Universite Pierre et Marie Curie Tour 22-23, 1er Etage 75242 PARIS CEDEX 05 Tel: +(33) 01-44-27-40-53 Fax: +(33) 01-44-27-41-17 e-mail silvi@lct.jussieu.fr Dear Dr. Jenkins, You can find such basis sets for pseudopotentials in J. Chem. Phys. 93, 7225 (1990) Eur. J. Mineral. 6, 7-16 (1994) sincerely Bernard SILVI Dear Dr. Jenkins, You can replace pseudo potential by standards core orbitals taken from the 6-311G set. Bernard SILVI Dear Professor Silvi, I have not done this type of thing before, I am not sure that the properties of the derivatives of the charge density will be preserved. But thankyou for the advice on the actual basis set to use. I am relatively new to localised basis sets. Best wishes, Samantha Jenkins The procedure is very safe, in fact we have used the valence orbitals of Pople as a starting point of exponent optimization with pseudopotentials. Which kind of derivatives? If it is the gradient of the charge density (McMaster the home of AIM) no problem, this is calculated by Carlo Gatti's program TOPOND98. If it is the derivatives with respect to nuclear coordinates this is not done by CRYSTAL98 (the Hellmann-Feynman theorem does not hold for localized basis functions). Bernard SILVI Dear Professor Silvi Thankyou for the extra information. I do infact use Carlo Gatti's code TOPOND98, I am interested in the derivatives higher than the gradient of rho. CRYSTAL01 calculates the derivatives with respect to the nuclear coordinates. I just obtained the referensec that you suggested, but they are for SiO2 and GeO2 not SiO and GeO. so presumably it will OK to optimise the outer expontents, whilst using the core form the bais set that you suggested? Thanks, Best wishes, Samantha jenkins From chemistry-request@server.ccl.net Wed Mar 7 12:21:25 2001 Received: from pegasus.arc.nasa.gov (pegasus.arc.nasa.gov [128.102.199.140]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27HLPw28596 for ; Wed, 7 Mar 2001 12:21:25 -0500 Received: (from ricca@localhost) by pegasus.arc.nasa.gov (8.11.1/8.11.1) id f27HLQI02084 for chemistry@ccl.net; Wed, 7 Mar 2001 09:21:26 -0800 (PST) Date: Wed, 7 Mar 2001 09:21:26 -0800 (PST) From: Alessandra Ricca Message-Id: <200103071721.f27HLQI02084@pegasus.arc.nasa.gov> To: chemistry@ccl.net Dear CCL members, We have two clusters of intel based machines. Cluster 1 * Intel Pentium III 600 MHz CPU with fan * ASUS P3B-F Motheroard * 512MB SDRAM PC100MHz (2x256MB), Cas III Type and Low Profile. * 22GB IBM IDE HDD 7200RPM * 4MB AGP ATI Display Card cluster 2 * (1)Intel Pentium III 800MHz CPU with fan, 256K cache * Intel L440GX+ Dual Pentium III Motherboard * SCSI, Lan and VGA on Board * 1024MB SDRAM PC100MHz (4x256MB), ECC Register * 40GB IBM IDE HDD 7200RPM We ran gaussian98 in parallel using linda on cluster 1 using redhat 6.1 for several months and everything appeared to function perfectly. Cluster 2 came with redhat 6.2, and initially everything seemed to be fine, so cluster 1 was upgraded to 6.2. Under 6.2 gaussian jobs fail on cluster 1 with a relatively short mean time between failure. We have now discovered that cluster 2 also seems to have problems under 6.2, but the mean time between failures is much longer. The failures come in two types: 1) the calculation appears to run but values are all garbage (the values print as "nan") 2) one of the processes dies, most commonly, the message is process 0 failed to complete. Before restoring 6.1 to the machine, does anyone know what this problem is and how to fix it? Thanks, Alessandra --------------------------------------------------------------------- Alessandra Ricca Mail: NASA Ames Research Center Senior Research Scientist Mail Stop 230-3 ELORET Corporation Moffett Field, CA 94035-1000 http://www.eloret.com Ph: +1-650-604-5410 Email: ricca@pegasus.arc.nasa.gov Fax: +1-650-604-0350 From chemistry-request@server.ccl.net Wed Mar 7 13:58:59 2001 Received: from france.chem.duke.edu (france.chem.duke.edu [152.3.169.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27Iwxw29353 for ; Wed, 7 Mar 2001 13:58:59 -0500 Received: from primo.chem.duke.edu (primo.chem.duke.edu [152.3.170.1]) by france.chem.duke.edu (8.9.3/8.9.3) with ESMTP id NAA17669; Wed, 7 Mar 2001 13:59:01 -0500 (EST) Received: from localhost (andres@localhost) by primo.chem.duke.edu (8.9.3+Sun/8.9.1) with ESMTP id NAA05464; Wed, 7 Mar 2001 13:59:00 -0500 (EST) X-Authentication-Warning: primo.chem.duke.edu: andres owned process doing -bs Date: Wed, 7 Mar 2001 13:59:00 -0500 (EST) From: Gerardo Andres Cisneros To: Alessandra Ricca cc: chemistry@ccl.net Subject: Re: No Subject Given By The Author In-Reply-To: <200103071721.f27HLQI02084@pegasus.arc.nasa.gov> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello We have a similar problem, we've just built an 8 node PIII cluster running RH6.2 (2.2.16-3 kernel) and I'm testing gaussian using Linda for this cluster. However, if the calculation takes more than 1 hour, invariably, one of the slave nodes will run out of memory because gaussian will fail to kill the processes so there will be a good number of phantom processes on the nodes just sitting there occupying memory. I would really appretiate if you could post a summary from any reply you might get. Thanks in advance Andres -- G. Andres Cisneros Department of Chemistry Duke University andres@chem.duke.edu From chemistry-request@server.ccl.net Wed Mar 7 13:35:44 2001 Received: from hotmail.com (f61.law9.hotmail.com [64.4.9.61]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27IZhw29201 for ; Wed, 7 Mar 2001 13:35:44 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 7 Mar 2001 10:33:45 -0800 Received: from 151.197.239.69 by lw9fd.law9.hotmail.msn.com with HTTP; Wed, 07 Mar 2001 18:33:45 GMT X-Originating-IP: [151.197.239.69] From: "James Ianni" To: chemistry@ccl.net Subject: New version of KINTECUS modeling software Date: Wed, 07 Mar 2001 13:33:45 -0500 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 07 Mar 2001 18:33:45.0570 (UTC) FILETIME=[249C4420:01C0A735] Powerful Industrial Strength/Research Grade chemical modeling software for simulation of combustion, nuclear, biological, atmospheric and many other processes. There are many new features. One prime feature is the ability to quickly run Chemkin/SENKIN II/III models without the use of supercomputing power or FORTRAN compiling/linking. Multiple Chemkin/freestyle thermodynamic databases can be used. Isothermal/Non-isothermal, adiabatic constant volume, constant pressure (variable volume) can easily be modeled with a flick of a switch. Programmed volume (replicating engine piston motion), programmed temperature, programmed species concentration can all easily be included in your model WITHOUT C/FORTRAN programming. Heterogeneous chemistry is also easily modeled. Chemkin II/III does NOT allow all these features. There are many other new features, included examples and much better documentation (see the KINTECUS_V2.pdf file) . Added by jkl: vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv It is available in http://www.ccl.net/cca/software/MS-WIN95-NT/kintecus/ or ftp://ftp.ccl.net/pub/chemistry/software/MS-WIN95-NT/kintecus/ Retrieve file Kintecus_V20.zip and unzip it. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Wed Mar 7 13:46:39 2001 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27Ikdw29271 for ; Wed, 7 Mar 2001 13:46:39 -0500 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer); Wed, 7 Mar 2001 18:46:38 +0000 Reply-To: "a.oganov" From: "Artem R. Oganov" To: CHEMISTRY Subject: CCL: DFT and Mott insulators again Date: Wed, 7 Mar 2001 18:45:20 -0000 Message-ID: BlankDear all, There were some problems with the appearance of my e-mail as some people got mysterious attachments which I did not send. Now I hope that my message will be read without problems, and I will get some replies. Many people have asked me to summarise replies, which I'll gladly do in case of any replies (so far I had none). Looking forward to hearing from you, Artem P.S. See the original question below: +++++++++++++++++++++++++++++++++++++++++++++++ Dear CCLers, I have the following question: It is known that DFT within the LDA and GGA gives no band gap for such transition metal oxides as FeO, CoO, NiO, which in fact are insulators (Mott insulators). Are there any ideas about how serious this error is? I suspect that there may be no real error: I understand that Kohn-Sham eigenvalues and electronic density of states are, strictly speaking, meaningless. Therefore, the absence of a band gap does not mean anything - even more it does not mean that the material is a metal. There might be other, more rigorous, ways to calculate the electrical conductivity from DFT - but I am not aware of any such work. On the other hand, GGA and LDA are known to reproduce many properties (elastic constants, equation of state, magnetic ordering, magnetic moments) of these oxides really well - at nearly the same level as they reproduce the properties, e.g., of MgO or NaCl. I would like to hear your ideas on: 1. The applicability of LDA/GGA to Mott insulators: can we use DFT at all, what we can and what we cannot calculate. 2. If there is any error at all, how serious it is. 3. How to calculate the electrical conductivity from DFT. Were such calculations done for any of the Mott insulators? 4. What is the best way of treating Mott insulators, especially at high pressures? LDA+U seems to be not too reliable at high pressures. Hartree-Fock would definitely give a band gap - but it gives it even for the free electron case! What else does exist? I will summarise replies on request. Cheers, Artem R. Oganov ----------------------------------------------------- Artem R. Oganov Department of Geological Sciences University College London Gower Street London WC1E 6BT tel: +44 (020)-7679-3344 fax: +44 (020)-7387-1612 email: a.oganov@ucl.ac.uk http://slamdunk.geol.ucl.ac.uk/~artem --------------------------------------------------- From chemistry-request@server.ccl.net Wed Mar 7 15:30:07 2001 Received: from dalton.quimica.unlp.edu.ar (dalton.quimica.unlp.edu.ar [163.10.18.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27KU3w29862 for ; Wed, 7 Mar 2001 15:30:05 -0500 Received: from bilbo.quimica.unlp.edu.ar (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.10.2/8.10.2) with ESMTP id f27LeMi02914 for ; Wed, 7 Mar 2001 17:40:22 -0400 Message-Id: <4.3.2.7.0.20010307162027.00a9f8e0@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Wed, 07 Mar 2001 17:29:33 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: Re: CCL:No Subject Given By The Author In-Reply-To: References: <200103071721.f27HLQI02084@pegasus.arc.nasa.gov> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi all, We have a five-node, heterogeneous cluster of pentium boxes. All of these have RH 6.0 but the kernel was updated to 2.2.16. Since we don't have pgf77 Gaussian sent us the binaries, so we didn't compile the program. Linda version is 3.1. All is working fine. Many of our calculations take several days to converge and we didn't note any problem related to memory or phantom process. It seems that migrating from RH 6.0 to 6.2 would be the problem (I don't kown why, though). Regards, Reinaldo From chemistry-request@server.ccl.net Wed Mar 7 17:15:08 2001 Received: from seagoon.newcastle.edu.au (seagoon.newcastle.edu.au [134.148.24.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27MF6w30497 for ; Wed, 7 Mar 2001 17:15:06 -0500 Received: from mail.newcastle.edu.au (renate-bio.newcastle.edu.au [134.148.66.13]) by mail.newcastle.edu.au (PMDF V5.2-32 #35875) with ESMTP id <0G9U00MMJLSSPQ@mail.newcastle.edu.au> for CHEMISTRY@ccl.net; Thu, 8 Mar 2001 09:14:53 +1100 (EST) Date: Thu, 08 Mar 2001 09:12:31 +1100 From: Renate Griffith Subject: ACS classification codes? To: CHEMISTRY@ccl.net Message-id: <3AA6B250.85F5D74F@mail.newcastle.edu.au> Organization: University of Newcastle MIME-version: 1.0 X-Mailer: Mozilla 4.73C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Dear all, I want to submit a manuscript to Molecular Simulation and they want you to give keywords using the ACS classification codes. I have searched the ACS website and can't find those codes. Can anybody help? Thanks Renate -- Dr. Renate Griffith, Lecturer, Discipline of Biological Sciences School of Biological and Chemical Sciences Institute of Life Sciences, Life Sciences Building, LS 46 The University of Newcastle Callaghan, NSW 2308, Australia Email: renateg@mail.newcastle.edu.au Phone: +61 2 4921 6990 Fax: +61 2 4921 6923 From chemistry-request@server.ccl.net Wed Mar 7 22:59:22 2001 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f283xJw32242 for ; Wed, 7 Mar 2001 22:59:21 -0500 Received: from iris.sipp.ac.cn [202.127.25.123] by iris.sipp.ac.cn with ESMTP (SMTPD32-6.04) id A55270401DA; Thu, 08 Mar 2001 12:06:42 +0800 Sender: user@ccl.net Message-ID: <3AA702B5.AD013E81@iris.sipp.ac.cn> Date: Thu, 08 Mar 2001 11:55:33 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: question about MD in Xplor Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All: I met a problem when runing MD in Xplor. I used the following input in the MD section, but the protein was blew like a balloon. I wonder what wrong with it. Thanks in advance. ------------------ vector do (fbeta=100) (all) dynamics verlet nstep=50000 timestep=0.001 iasvel=maxwell firsttemperature=300 nprint=25 tcoupling=true tbath=300 trajectory=dynamic.dcd nsavc=500 end ----------------------------------- Regards, mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Mar 7 16:38:53 2001 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f27Lcqw30314 for ; Wed, 7 Mar 2001 16:38:52 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Wed, 7 Mar 2001 22:40:15 +0100 Received: from zorn.bmc.uu.se (IDENT:spoel@zorn.bmc.uu.se [130.238.37.95]) by XRAY.bmc.uu.se (8.9.3/8.8.7) with ESMTP id WAA16235 for ; Wed, 7 Mar 2001 22:42:04 +0100 Date: Wed, 7 Mar 2001 22:38:51 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: chemistry@ccl.net Subject: rh6.2 problems. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Everyone running rh6.2 with the stock kernel (2.2.14 something) should upgrade the kernel to either 2.2.16-3 or 2.2.17 something. rh 2.2.14 will give random floating point errors. this is a faq Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++