From chemistry-request@server.ccl.net Wed May 5 09:39:37 1999 Received: from classic.chem.msu.su (classic.chem.msu.su [158.250.32.143]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA32520 for ; Wed, 5 May 1999 09:39:34 -0400 From: gran@classic.chem.msu.su Received: from localhost ( [127.0.0.1] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Wed, 5 May 1999 17:34:36 MSK-3MSD-4,3,5,0,7200,10,5,0,10800 Message-Id: <199904051734.3626230.8@classic.chem.msu.su> Date: Wed, 05 May 1999 17:18:41 +0400 To: CHEMISTRY@ccl.net Cc: gamess-users@Glue.umd.edu, qcnt@onelist.com Subject: PC GAMESS version 5.2 is available X-Mailer: MR/2 Internet Cruiser Edition for OS/2 v1.60 b60 (Unregistered) Dear GAMESS users, New PC GAMESS version 5.2 has been released and is currently available from the PC GAMESS www and ftp sites (soon it will also be available from the official GAMESS www and ftp servers). As compared to the previous public PC GAMESS version 5.1, the main new features are as follows: It is now possible to run the PC GAMESS under Linux; New RHF MP4(SDTQ) (i.e., full MP4) energy module is added. It seems that the PC GAMESS implementation of MP3/MP4 energies is the fastest among those currently available on Intel platform, see http://classic.chem.msu.su/gran/gamess/performance.html for details; The SMP scaling properties of MP3/MP4 calculations are improved considerably; The speed of MP2 gradient calculations for non-abelian symmetry groups is increased; The speed of Conjugated Gradient solver (used mainly during calculations of analytical second derivatives) is improved significantly; The Finite field module is changed to avoid reevaluations of 2-e integrals if possible; The ECP integrals module is rewritten to avoid numerical instability problems. For further information, see the URLs http://classic.chem.msu.su/gran/gamess/index.html http://quantum-2.chem.msu.ru/gran/gamess/index.html Yours sincerely, Alex. A. Granovsky, Laboratory of Chemical Cybernetics, Moscow State University From chemistry-request@server.ccl.net Wed May 5 11:33:29 1999 Received: from avi.llnl.gov (avi.llnl.gov [128.115.211.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA01028 for ; Wed, 5 May 1999 11:33:28 -0400 Received: from localhost (ers@localhost) by avi.llnl.gov (8.8.7/8.8.7) with ESMTP id IAA10561; Wed, 5 May 1999 08:20:11 -0700 Date: Wed, 5 May 1999 08:20:11 -0700 (PDT) From: Eric Schwegler Reply-To: schwegler1@llnl.gov To: fparnold@balihai.uchicago.edu cc: CLJANSS@sandia.gov, chemistry@server.ccl.net Subject: MPQC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Fred, Just wanted to let you know that Curt Janssen is still maintaining (and improving) MPQC at Sandia. I know he has made several major improvements to the code over the last few years, so you should contact him to get the latest version. I believe his email address is: CLJANSS@sandia.gov -Eric -- Eric Schwegler Lawrence Livermore National Laboratory P.O. Box 808, L-415 Livermore, CA 94551 --------------------------------------- email: schwegler1@llnl.gov phone: 925-424-3098 fax: 925-422-6594 Hello, We've recently found the program MPQC (Massively Parallel Quantum Chemistry) by Curtis Janssen, et al., and some of the researchers (read: graduate students) expressed an interest in it, due its support for distributed parallel architecutures using MPI, excellent (theoretical) scaling, and the use of the GNU Public License. (We have a strong Debian movement at U. of C.) However, the code seems to have frozen two years ago, the C++ is already succumbing to software rot, and the authors are uncontactable. Has anyone done any work on this package, or know its present status? Under the GPL, we could theoretically start banging on it (at least move it from libg++ to libstdc++), but I'd like to know what its authors' plans are first. -Fred Sb: Antimony Frederick P. Arnold, Jr. Mass: 121.75 Advanced Research Systems@U. Chicago MP: 630.5 Deg C 5640 S. Ellis Ave Electronegativity: 1.82 Chicago, IL 60637A From chemistry-request@server.ccl.net Wed May 5 21:41:06 1999 Received: from toucan.phy.bris.ac.uk (toucan.phy.bris.ac.uk [137.222.30.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA06088 for ; Wed, 5 May 1999 21:41:05 -0400 Received: from localhost (guido@localhost) by toucan.phy.bris.ac.uk (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id CAA08888; Thu, 6 May 1999 02:36:12 +0100 (BDT) Date: Thu, 6 May 1999 02:36:11 +0100 From: Guido Germano Sender: guido@toucan.phy.bris.ac.uk To: Peter Varnai cc: Computational Chemistry List , help@gaussian.com Subject: Re: CCL:PCM with MP2 In-Reply-To: <199903130201.CAA29424@bellatrix.pcl> Message-ID: Organization: Physics Department University of Bristol MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 13 Mar 1999, Peter Varnai wrote to chemistry@www.ccl.net: > Has anyone succeeded in calculating PCM solvation > energy with MP2 density? According to the gaussian98 > manual it is possible... The "EUMP2" energy I got is the same both when scrf=pcm,etc. is in the command line and when it isn't. Also according to the g94 manual PCM and MP2 are available together: I think it's an old documentation bug. Btw this is not the only sloppy point of the g98 manual about the PCM method: e.g. only a few of the variables that can be set with the "read" option are actually listed. To find out the true capabilities of the program you must open the source code and know Italian. :-O Guido Germano University of Bristol, England tel. +44-117-928 8755, fax +44-117-9255624 http://www.phy.bris.ac.uk/staff/germano_g.html From chemistry-request@server.ccl.net Wed May 5 23:00:52 1999 Received: from kimia.um.edu.my ([202.185.71.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA07116 for ; Wed, 5 May 1999 23:00:44 -0400 Received: by kimia.kimia.um.edu.my (5.x/SMI-SVR4) id AA03715; Thu, 6 May 1999 10:52:18 +0800 Date: Thu, 6 May 1999 10:52:17 +0800 (MYT) From: "Dr. Ibrahim Noorbatcha" To: chemistry@ccl.net Subject: Transition state search Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody. Given a potential energy function of a molecular system, are there any software available which can locate the transition state?. I remember that a similar question has been posted in this list before. However I could not locate the replies. Can anybody give me some pointers, please?. Thank you very much for your replies. ibrahim ============================================================================ Dr. Ibrahim Ali Noorbatcha Email: ibrahim@kimia.um.edu.my Department of Chemistry Phone: 603-759-4260 Universiti Malaya Fax : 603-759-4193 50603 Kuala Lumpur Malaysia ============================================================================= From chemistry-request@server.ccl.net Tue May 4 19:09:39 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA25726 for ; Tue, 4 May 1999 19:09:39 -0400 Received: from web108.yahoomail.com (web108.yahoomail.com [205.180.60.75]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA22180 Tue, 4 May 1999 19:05:04 -0400 (EDT) Message-ID: <19990504230539.4811.rocketmail@web108.yahoomail.com> Received: from [129.6.113.104] by web108.yahoomail.com; Tue, 04 May 1999 16:05:39 PDT Date: Tue, 4 May 1999 16:05:39 -0700 (PDT) From: anstrom nanometer Subject: clustering of a huge number of conformations To: CHEMISTRY@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, I have a huge number of conformations to cluster (~60k). Since all clustering algorithm that I know need to calculate pair-wise distances between every two conformations, it will be an unsurmountable big space for my computer's memory (14.4G). I figured out an alternative way to implement it, but the clutering result was found not a optimal solution, i.e. for example, 260 clusters were generated by my way instead of the expected 236 clusters generated by the original algorithm. I would appreciate receiving any of your knowledge on this subject. Hongyu Zhang CARB, U. of Maryland _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From chemistry-request@server.ccl.net Tue May 4 16:04:52 1999 Received: from dqo.fcq.unc.edu.ar (root@dqo.fcq.unc.edu.ar [200.16.18.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA24202 for ; Tue, 4 May 1999 16:04:50 -0400 Received: from fer-net.fcq.unc.edu.ar (marcos@[200.16.18.99]) by dqo.fcq.unc.edu.ar (8.8.7/8.8.7) with SMTP id RAA06499; Tue, 4 May 1999 17:03:30 -0300 From: Marcos Villarreal Organization: UNC, Dpto. Qca. Biol.-CIQUIBIC To: chemistry@ccl.net Subject: Animating CHARMM vibrations Date: Tue, 4 May 1999 04:50:03 -0400 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain Cc: charmm-bbs@csir.org MIME-Version: 1.0 Message-Id: <99050404553702.01828@fer-net.fcq.unc.edu.ar> Content-Transfer-Encoding: 8bit Hello! What program could I use in order to animate vibrations calculated with CHARMM. Thanks in advance. -- Lic. Marcos Villarreal Dpto Quimica Biologica Universidad Nacional de Cordoba Cordoba. Argentina