From Gerald.Loeffler@univie.ac.at Mon Sep 8 03:22:52 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id CAA00046; Mon, 8 Sep 1997 02:47:48 -0400 (EDT) Received: from gerilap.imp.univie.ac.at (gerilap.imp.univie.ac.at [131.130.80.125]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id IAA17634; Mon, 8 Sep 1997 08:46:33 +0200 Message-ID: <34139DB3.6633@univie.ac.at> Date: Mon, 08 Sep 1997 08:39:47 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@univie.ac.at Organization: I.M.P. X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: Ahmed Bouferguene CC: chemistry@www.ccl.net Subject: Java Full Multigrid Framework (was: Elliptic Equations) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Let me take this opportunity to announce a small (and hopefully useful) piece of software I've written to solve linear elliptic partial differential equations (PDE's) on a regular finite-difference grid in 3D. This is called the Full Multigrid (FMG) framework, because it is written in the style of a framework in Java 1.1 and uses the FMG algorithm, which is usually considered the most efficient general-purpose algorithm for solving PDE's. Documentation exists in the form of javadoc-generated HTML files and is online at http://www.imp.univie.ac.at/Loeffler/Javadoc. There is also a paper that will appear in the proceedings of ISCOPE97, to be held in Dec. 1997 in California. The paper is accessible from my home-page, too, and cites some other books (most notably the Multigrid Tutorial published by SIAM) that I found useful when learning the FMG algorithm. Write me an email if you are interested in this (yet fairly unproven!) software. gerald Ahmed Bouferguene wrote: > > Hi all, > > Does anybody know a reference (paper, book, ...) dealing with > elliptic partial differential equations in 3D. > > I will appreciate your help. > > Ahmed Bouferguene > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: boufer@cennas.nhmfl.gov > -- Original Sender From: Address: boufer@CeNNAs.nhmfl.gov > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html -- Gerald Loeffler PostDoc in Theoretical Biophysics EMail: Gerald.Loeffler@univie.ac.at WWW: http://www.imp.univie.ac.at/Loeffler Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From Lutz.Ehrlich@EMBL-Heidelberg.de Mon Sep 8 05:22:59 1997 Received: from stork.EMBL-Heidelberg.DE for Lutz.Ehrlich@EMBL-Heidelberg.de by www.ccl.net (8.8.3/950822.1) id FAA00536; Mon, 8 Sep 1997 05:02:10 -0400 (EDT) Received: from cuckoo.embl-heidelberg.de (cuckoo.EMBL-Heidelberg.DE [192.54.41.16]) by stork.EMBL-Heidelberg.DE (8.8.4/8.8.4) with ESMTP id LAA16929; Mon, 8 Sep 1997 11:02:10 +0200 (MDT) Received: by cuckoo.embl-heidelberg.de (8.7.1) id JAA16200; Mon, 8 Sep 1997 09:02:09 GMT Date: Mon, 8 Sep 1997 11:02:09 -6000 From: Lutz Ehrlich To: Verschelde Jean-Luc cc: chemistry@www.ccl.net Subject: Re: CCL:relative solvent accessible surface In-Reply-To: <322D9DA6.41C6@rug.ac.be> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Jean-Luc. > What software package is able to calculate the relative solvent > accessible surface of proteins ? Check out http://www.embl-heidelberg.de/Services/argos/ASC.21/asc2.html ASC is a package that is shell-oriented. If you want to use the software >from within your own programs, use the NSC package http://www.embl-heidelberg.de/Services/argos/ASC.21/nsc2-down.html I wrote a Python wrapper for NSC which is fully interfaced with Konrad Hinsen's Molecular Modelling Toolkit (http://starship.skyport.net/crew/hinsen/mmtk.html). With this you can query your proteins/macromolecules for their surface. Feel free to contact me if you're interested. Cheers, Lutz --------------------- Lutz Ehrlich Structural Biology EMBL Meyerhofstr. 1 D-69012 Heidelberg Germany email: lutz.ehrlich@embl-heidelberg.de web : http://www.embl-heidelberg.de/~ehrlich phone: +49-6221-387-140 fax : +49-6221-387-517 From wibke@theochem.uni-duesseldorf.de Mon Sep 8 08:22:53 1997 Received: from lithium.theochem.uni-duesseldorf.de for wibke@theochem.uni-duesseldorf.de by www.ccl.net (8.8.3/950822.1) id IAA01215; Mon, 8 Sep 1997 08:13:06 -0400 (EDT) Received: from caesium.theochem.uni-duesseldorf.de (caesium.theochem.uni-duesseldorf.de [134.99.82.7]) by lithium.theochem.uni-duesseldorf.de (8.8.3/8.8.3) with ESMTP id OAA11488; Mon, 8 Sep 1997 14:10:20 +0200 (MET DST) Received: (from wibke@localhost) by caesium.theochem.uni-duesseldorf.de (8.8.3/8.8.3) id OAA19160; Mon, 8 Sep 1997 14:10:20 +0200 (MET DST) Date: Mon, 8 Sep 1997 14:10:20 +0200 (MET DST) From: Wibke Sudholt Message-Id: <199709081210.OAA19160@caesium.theochem.uni-duesseldorf.de> To: chemistry@www.ccl.net Subject: CASSCF/CASPT2 question Cc: wibke@lithium.theochem.uni-duesseldorf.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: LrRRQ6/YT50Gy061+qSyFg== Dear CCLers, perhaps someone of you can help me with this problem: I am doing excited state CASPT2 calculations with a CASSCF reference on a medium size organic molecule. Sometimes different starting orbitals lead to different CASSCF results probably because of several wavefunction minima. I suppose that this can be caused by an unsufficient active space, but I would run out of time and computational resources if I enlarge it. I also do not want to use state average calculations. So I need a systematic criterion to choose safely the "right" results. I am thinking of the lowest CASSCF energy (variation principle) or the highest weight of the CASSCF reference in the CASPT2 calculation (lowest perturbation). What would you prefer? Or are there other criterions? Can I compare calculations with different active spaces in the same way? I hope this question is not too stupid, but the subject is still relatively new to me. Any suggestions or pointers to the literature would be welcome. I will try to summerize. Thank you very much in advance Dipl.-Chem. Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf Germany wibke@theochem.uni-duesseldorf.de From RPO@tifrvax.tifr.res.in Mon Sep 8 11:22:52 1997 Received: from tifrvax.tifr.res.in for RPO@tifrvax.tifr.res.in by www.ccl.net (8.8.3/950822.1) id KAA01908; Mon, 8 Sep 1997 10:29:59 -0400 (EDT) Received: from tifrvax.tifr.res.in by tifrvax.tifr.res.in (PMDF #12198) id <01INEUJKGL740024BE@tifrvax.tifr.res.in>; Mon, 8 Sep 1997 19:59 +0530 Date: Mon, 8 Sep 1997 19:59 +0530 From: "DR. RAJENDRA PRASAD OJHA" Subject: Request To: chemistry@www.ccl.net Message-id: <01INEUJKGL740024BE@tifrvax.tifr.res.in> X-VMS-To: IN%"chemistry@www.ccl.net" X-VMS-Cc: RPO I work with Dr. Ojha. We have AMBER4.0 at Gorakhpur University India. I have a problem in running amber. After dynamics of a dna molecule both strands are melted. One way is to put some distance constrain for the hydrogen bonds. Is there any direct methodwith out using constraints so that it should not melt. It is melting in both cases, in absence and presence of ions. If so please write me and oblige. Yours sinceerely R.K. Tiwari From dietmar.kaiser@uni-tuebingen.de Mon Sep 8 13:22:56 1997 Received: from outmail.zdv.uni-tuebingen.de for dietmar.kaiser@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id MAA02357; Mon, 8 Sep 1997 12:25:35 -0400 (EDT) Received: from by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AB18126; Mon, 8 Sep 97 18:25:32 MES Received: from commlink.zdv.uni-tuebingen.de by mailserv.uni-tuebingen.de with SMTP (PP); Mon, 8 Sep 1997 18:19:03 +0200 Received: (from coika01@localhost) by commlink.zdv.uni-tuebingen.de (8.6.12/8.6.12) id SAA15147; Mon, 8 Sep 1997 18:19:02 +0200 Date: Mon, 8 Sep 1997 18:19:02 +0200 (MESZ) From: Dietmar Kaiser To: chemistry@www.ccl.net Subject: CCL:Gaussian:Derivative Info from Freq.Calc. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, sorry if this is a too simple question, but where in the output of a G94 frequency calculation can I find the derivative D2E/DX2 that is read in by opt=readfc from the checkpoint file? Thanks a lot, Dietmar ########################################################################### # # # Dietmar Kaiser # # Universitaet Tuebingen # # Inst. fuer Organische Chemie # # Auf der Morgenstelle 18 Tel. 07071/29-78736 FAX 07071/29-6925 # # D-72076 Tuebingen e-mail dietmar.kaiser@uni-tuebingen.de # # Germany # # # ###########################################################################