From chemistry-request@ccl.net Wed Feb 4 08:52:37 2004 Received: from hartree4.UGent.be (hartree4.ugent.be [157.193.91.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i14DqaU6024097 for ; Wed, 4 Feb 2004 08:52:36 -0500 Received: from hartree4.UGent.be (localhost [127.0.0.1]) by hartree4.UGent.be (8.12.8/8.12.8) with ESMTP id i14DxKXU003359 for ; Wed, 4 Feb 2004 14:59:20 +0100 Received: from localhost (tom@localhost) by hartree4.UGent.be (8.12.8/8.12.8/Submit) with ESMTP id i14DxCCA003355 for ; Wed, 4 Feb 2004 14:59:19 +0100 Date: Wed, 4 Feb 2004 14:59:12 +0100 (CET) From: Tom Kuppens To: CHEMISTRY^at^ccl.net Subject: G03 with Linda Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi there, I compiled g03revB05 with TCP Linda 7.1 Rev7.1 with PGI5.1 on Redhat 8.0. I also tried to do this on RedHat9.0. I managed to compile g03 on RH9 (after some tweaks grrr) but the compilation of linda goes wrong (d*mn glibc). I contacted Gaussian helpdesk and they advised me to use the RH8.0 binaries on the RH9.0. So far so good. Now ... How do you get Linda to work? There is virtually no documentation to get it running. I tried everything that I could think of to run a gaussianjob in parallel with linda but they all failed. We are working on PIV's RH9.0. - user that is running gaussian has rsh access to other nodes and vice versa (btw why not ssh? Far more easier an safer ..) - .tsnet.config file created in user's ~/ - $g03root is on all the machines equivalent ie /usr/local - gaussian input was put on a NFS share and SCR files were written on this NFS share (accessible to all nodes) Gaussian jobs are submitted without a problem/errors (%NPROCLINDA=2) but the process doesn't migrate. (All nodes are behind a switch and are connected via 100MBit ethernet.) Can someone give me some hints on what's going wrong, and is there someone who can point me out what to do ... ? Thanks in advance!! Tom Kuppens Research group Quantumchemistry Department of Inorganic and Physical Chemistry WE06V Ghent University Krijgslaan 281 - S3, 9000 Ghent, Belgium Tel +32(0)9 264 4444 Fax +32(0)9 264 4983 -- http://allserv.UGent.be/~tkuppens ---- Running is not just a sport but a biological necessity. -- Yiannis Kouros From chemistry-request@ccl.net Wed Feb 4 07:29:18 2004 Received: from fitch6.uni2.net (fitch6.uni2.net [130.227.52.109]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i14CTGU6021831 for ; Wed, 4 Feb 2004 07:29:17 -0500 Received: from HLUSF26A.lundbeck.com ([130.227.160.123]) by fitch6.uni2.net (8.12.6/8.11.6) with SMTP id i14CVafY005896 for ; Wed, 4 Feb 2004 13:31:37 +0100 Received: from ([172.16.0.163]) by HLUSF26A.lundbeck.com; Wed, 04 Feb 2004 13:31:03 +0100 (CET) Received: FROM ludk0006.lundbeck.com BY ludk0163.lundbeck.com ; Wed Feb 04 13:31:29 2004 +0100 Received: by ludk0006.lundbeck.com with Internet Mail Service (5.5.2657.72) id <1HBZ5MP2>; Wed, 4 Feb 2004 13:31:31 +0100 Message-ID: From: Jan Torleif Pedersen To: chemistry)at(ccl.net Subject: Snake plot program Date: Wed, 4 Feb 2004 13:31:26 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Greetings, I am looking for a program that is able to make snake like plots for protein sequences of transmembrane proteins. Is anyone here aware of such programs ? Regards -- Jan Dr. Jan Torleif Pedersen Section head, Bioinformatics Department of Molecular Genetics H. Lundbeck A/S Ottiliavej 9, 2500 DK-Valby Denmark phone: +45 36 43 28 87 FAX: +45 36 43 82 53 email: jatp)at(lundbeck.com From chemistry-request@ccl.net Wed Feb 4 19:12:02 2004 Received: from lito.mit.edu (LITO.MIT.EDU [18.82.2.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i150C2U6010389 for ; Wed, 4 Feb 2004 19:12:02 -0500 Received: from localhost (damian@localhost) by lito.mit.edu (8.11.6/8.11.6) with ESMTP id i150FE329037 for ; Wed, 4 Feb 2004 19:15:26 -0500 Date: Wed, 4 Feb 2004 19:15:14 -0500 (EST) From: Damian Scherlis To: CHEMISTRY!at!ccl.net Subject: CCL: IPCM and charge-renormalization in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, when PCM is used on a charged solute in Gaussian, the polarization charge is normalized to be consistent with the Gauss Law, with the normalization method selected by the command ICOMP. What is the default renormalization method in the case of IPCM. Is it possible to change it? How? Many thanks in advance, ------------------------ Damian Scherlis Department of Materials Science & Engineering Massachusetts Institute of Technology damian!at!lito.mit.edu 617 253 6026