From chemistry-request@server.ccl.net Thu Jul 4 04:40:26 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g648eQS12278 for ; Thu, 4 Jul 2002 04:40:26 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 17Q26N-0007TC-00; Thu, 04 Jul 2002 08:36:35 +0000 Date: Thu, 4 Jul 2002 08:36:35 +0000 (GMT) From: Szilveszter Juhos To: Fdo Danilo Gonzalez Nilo cc: chemistry@ccl.net Subject: Re: CCL:CHARMm with LAM-MPI In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 3 Jul 2002, Fdo Danilo Gonzalez Nilo wrote: > Any body know some program to check all CPU in cluster? (some thing like > "top" command ) rrdtool ( http://www.rrdtool.com/ ) or ganglia ( see http://ganglia.mrcluster.org/ for demo and click on the left upper corner for source ) does something similar. Condor is an other queueing system that can be used also and it has monitoring web-interface as well : http://www.cs.wisc.edu/condor/ Szilva From chemistry-request@server.ccl.net Thu Jul 4 05:56:45 2002 Received: from angelo.kcl.ac.uk ([137.73.66.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g649uiS13917 for ; Thu, 4 Jul 2002 05:56:44 -0400 Received: from kcl.ac.uk (pc205-29.pcy.kcl.ac.uk [137.73.205.29]) by angelo.kcl.ac.uk with ESMTP id g649uicF009427 for ; Thu, 4 Jul 2002 10:56:44 +0100 (BST) Message-ID: <3D2411E1.9EB6A07A@kcl.ac.uk> Date: Thu, 04 Jul 2002 10:14:09 +0100 From: SCT Organization: KCL X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "CCL (Computational Chemistry List)" Subject: SIESTA Restart Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, Is there anybody who knows how to exactly restart a SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) calculation? Thank you. Best regards, Sigrid Tuble King's College London From chemistry-request@server.ccl.net Thu Jul 4 07:42:35 2002 Received: from ovlev1.mdche.u-szeged.hu ([160.114.101.231]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g64BgVS16498 for ; Thu, 4 Jul 2002 07:42:32 -0400 Received: from localhost by ovlev1.mdche.u-szeged.hu (5.65v3.2/1.1.10.5/19Nov99-0914AM) id AA05249; Thu, 4 Jul 2002 13:49:38 +0100 Date: Thu, 4 Jul 2002 13:49:38 +0100 (GMT+0100) From: Csaba Hetenyi To: chemistry@ccl.net Subject: properties of ligand-protein binding Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Could you recommend free programs for the calculations of the follwing properties: -the fraction of the ligand volume buried inside the binding pocket, -the size of lipophilic cavities along the protein-ligand interface, -the solvent-accessible surface (SAS) of nonpolar parts of the ligand, and -the number of close contacts between non-hydrogen-bonded polar atoms of the ligand and the protein? Any contribution is appreciated. Programs will be summarized. Best wishes, Csaba _______________________________________ Csaba Hetenyi, M.Sc., Ph.D. University of Szeged Dept. of Medical Chemistry Addr.:H-6720 Szeged, Dom ter 8, Hungary Tel.: +36-62545147 or: +36-62545136 Fax.: +36-62545971 From chemistry-request@server.ccl.net Thu Jul 4 04:19:44 2002 Received: from hotmail.com ([64.4.15.183]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g648JiS11768 for ; Thu, 4 Jul 2002 04:19:44 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 4 Jul 2002 01:19:39 -0700 Received: from 133.11.92.210 by lw10fd.law10.hotmail.msn.com with HTTP; Thu, 04 Jul 2002 08:19:39 GMT X-Originating-IP: [133.11.92.210] From: "warau kimura" To: chemistry@ccl.net Subject: PCM &CPCM in Gaussian98 Date: Thu, 04 Jul 2002 17:19:39 +0900 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 04 Jul 2002 08:19:39.0820 (UTC) FILETIME=[8AC3FEC0:01C22333] Dear CCLers, When I calculted the solvation energy of actinides using PCM model and CPCM model in Gaussian98, I met the following error: PEDRA: too many spheres; increase Omega Error termination via Lnk1e in /usr/local/src/g98/l502.exe. My calculating system is actinides, including both the first hydration shell and a full second hydration shell, totally 30 waters around actinide element. Could you please help me out on this problem? Your kind help would be greately appreciated. Kimura, The Dept. Quantum Engineering and Systems Science The University of Tokyo Japan _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From chemistry-request@server.ccl.net Thu Jul 4 11:46:59 2002 Received: from TheWorld.com ([199.172.62.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g64FkxS24049 for ; Thu, 4 Jul 2002 11:46:59 -0400 Received: from vaio.theworld.com (1Cust230.tnt12.bos10.da.uu.net [63.17.121.230]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id LAA21039 for ; Thu, 4 Jul 2002 11:46:58 -0400 Message-Id: <5.1.0.14.1.20020704114154.009f42b0@pop.theworld.com> X-Sender: jle@pop.theworld.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 04 Jul 2002 11:47:03 -0400 To: chemistry@ccl.net From: Joe Leonard Subject: re: C Hacker question - thanks! Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Thanks to all who replied to my question regarding how to get the name of the calling routine of a C function. It seems this is not "a simple thing", which is what I was afraid of. The most useful suggestion(s) were to treat the problem via #defining the call rather than have the routine figure out its caller: #define Error_Msg(x,y) Error_Msg_Linux(__func__,x,y) so that one could write Error_Msg("Unable to open output file",UNABLE_TO_OPEN) and the error message routine would see the calling function as the first argument. __FUNCTION__ seems to work as well in gcc, although __func__ conforms to the newer standard. This makes it easy for error messages to be tagged where they arise (which is what I was looking for). Research is currently underway on SGI - the older machines I have access to don't see to have either of these symbols. I'm making due with __FILE__ and __LINE__, which is not quite what I want (but it works). If anybody's familiar with a similar variable (or compiler switch setting) for IRIX C to get me what gcc yields, please post it! I want to keep using IRIX C as long as possible due to the performance gains which result. Thanks again to all - hopefully this helps somebody else with how to do nice error messages! Joe Leonard jle@theworld.com (formerly jle@world.std.com) From chemistry-request@server.ccl.net Thu Jul 4 12:04:11 2002 Received: from dirac.bri.nrc.ca ([206.167.189.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g64G4BS24462 for ; Thu, 4 Jul 2002 12:04:11 -0400 Received: from localhost (wujih@localhost) by dirac.bri.nrc.ca (SGI-8.9.3/8.9.3) with ESMTP id MAA96896; Thu, 4 Jul 2002 12:04:07 -0400 (EDT) X-Authentication-Warning: dirac.bri.nrc.ca: wujih owned process doing -bs Date: Thu, 4 Jul 2002 12:04:07 -0400 From: Jianhui Wu To: chemistry@ccl.net cc: amber@heimdal.compchem.ucsf.edu Subject: Origin300, Linux Cluster Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, I have a budget around $40k CN to shop for a new computer system, which will be used for MD simulation, virtual screening and some bioinformative stuff. Currently, I am looking at two options: Origin 300 (2 cpu) or PC Linux Cluster. I would like to hear your experience with these systems and spend the limited budget right. (1) An Origin 300 2cpu 500MHZ cost around $35k. Are you using this kind of system? Do you have benchmark of MD simulation (such as Amber) for this system? Do you regret your purchase? (2) What is the best configuration for a PC Linux cluster now? Is your cluster stable enough? For example, it only break down once a month instead of once a week or two weeks. How do you take care of the maintance issue? Do you keep a spare node to serve as spare parts for other nodes? How much it cost to mantain a PC cluster (service, parts, etc)? If you make the choice, what kind of system would you go for it? Any suggestion will be greatly appreciated. Best wishes, Jian Hui Wu From chemistry-request@server.ccl.net Thu Jul 4 12:32:36 2002 Received: from saumur.cnrs-orleans.fr ([163.9.6.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g64GWZS25195 for ; Thu, 4 Jul 2002 12:32:35 -0400 Received: (from hinsen@localhost) by saumur.cnrs-orleans.fr (8.11.2/8.11.2) id g64GU8h17552; Thu, 4 Jul 2002 18:30:08 +0200 Date: Thu, 4 Jul 2002 18:30:08 +0200 Message-Id: <200207041630.g64GU8h17552@saumur.cnrs-orleans.fr> X-Authentication-Warning: saumur.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: chemistry@ccl.net Subject: Announcement: Molecular Modeling Toolkit release 2.2 Molecular Modeling Toolkit release 2.2 ====================================== The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations. MMTK's functionality includes - construction of molecular systems, with special support for proteins and nucleic acids - infinite systems or periodic boundary conditions (orthorhombic elementary cells) - common geometrical operations on coordinates - rigid-body fits - visualization using external PDB and VRML viewers; animation of dynamics trajectories and normal modes - the AMBER 94 force field, with several options for handling electrostatic interactions - a deformation force field for fast normal mode calculations on proteins - energy minimization (steepest descent and conjugate gradient) - molecular dynamics (with optional thermostat, barostat, and distance constraints) - normal mode analysis - trajectory operations - point charge fits - molecular surface calculations - interfaces to other programs Release 2.2 contains numerous small additions, improvements, and bug fixes. The main new features since the last official release, 2.0, are - Parallelization on shared-memory machines using threads. - Parallelization using MPI. The parallelization uses a data replication scheme and is therefore efficient only for a relatively small number of processors. - Various harmonic force fields for efficient normal mode calculations on proteins. - Harmonic restraints. - OPLS force field. - TrajectoryViewer, a tool for inspecting MMTK trajectories. For more information and for downloading, see the MMTK Web site at http://dirac.cnrs-orleans.fr/MMTK/ or http://starship.python.net/~hinsen/MMTK/ See also: K. Hinsen The Molecular Modeling Toolkit: A New Approach to Molecular Simulations J. Comp. Chem. 21, 79-85 (2000) -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 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 Jul 4 21:10:35 2002 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g651AZS03137 for ; Thu, 4 Jul 2002 21:10:35 -0400 Received: from PACHA (el-402-03.ee.sc.edu [129.252.22.226]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2655.55) id M6C99ZVL; Thu, 4 Jul 2002 21:10:34 -0400 Message-ID: <011a01c223c0$945fbb30$e216fc81@PACHA> From: "derosa" To: Subject: chk files in gaussian 98 Rev. A.6 Date: Thu, 4 Jul 2002 21:09:14 -0400 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear all: I have several check point files from calculations with gaussian 98 Revision A.6. At this moment I do not have access to any revision before A.9. Is there any way I can reuse those chk? or my only option is to run everything again?. I know that if the I could use the utility formchk from revision A.6, I can get an fchk file that can be converted back into a chk file using the unfchk utility of any revision I want to use, but formchk from A.6 is not available to me. Thank you for your help Pedro ******************************** Dr. Pedro A. DEROSA Dept of Electrical Engineering University of South Carolina Off 2D33 Ph. (1-803) 777-8401 FAX (1-803) 777-8045 e-mail: derosa@engr.sc.edu ********************************