From chemistry-request@server.ccl.net Fri Oct 29 05:10:14 1999 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA04785 for ; Fri, 29 Oct 1999 05:10:14 -0400 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by mserv.rug.ac.be (8.9.0/8.9.0) with ESMTP id LAA17857 for ; Fri, 29 Oct 1999 11:06:15 +0200 (MET DST) Received: from houston (houston.rug.ac.be [157.193.89.160]) by allserv.rug.ac.be (8.9.3/8.9.3) with SMTP id LAA19482 for ; Fri, 29 Oct 1999 11:06:12 +0200 (MET DST) Received: by localhost with Microsoft MAPI; Fri, 29 Oct 1999 11:06:06 +0200 Message-ID: <01BF21FD.98DC4C40.jeanluc.verschelde@rug.ac.be> From: Verschelde Jean-Luc To: "'CCL'" Subject: proton affinity Date: Fri, 29 Oct 1999 11:06:05 +0200 Organization: Universiteit Gent X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Encoding: 17 TEXT Dear all, I need information about calculating the proton affinity of peptides. I also wonder if software packages are available that do this kind of calculation. Thanks. ----------------------------------------------------------------------------------------------------------------- Verschelde Jean-Luc Department of Medical Protein Research (VIB 09) and Department of Biochemistry, Faculty of Medicine, University Ghent, K.L. Ledeganckstraat 35 Ghent. Tel. 32 (9) 2645306 Fax. 32 (9) 2645279 E-mail: jeanluc.verschelde@rug.ac.be ---------------------------------------------------- From chemistry-request@server.ccl.net Fri Oct 29 07:09:47 1999 Received: from email.guomai.sh.cn (e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06138 for ; Fri, 29 Oct 1999 07:09:42 -0400 Received: from guomai.sh.cn ([202.96.206.30]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with ESMTP id <0FKD006ST2SPGR@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Fri, 29 Oct 1999 19:05:13 +0800 (CST) Date: Fri, 29 Oct 1999 18:39:00 +0800 From: Yubo Fan Subject: How to run G98 on AIX4.2 To: CHEMISTRY@ccl.net Message-id: <38197944.20532991@guomai.sh.cn> MIME-version: 1.0 X-Mailer: Mozilla 4.6 [en] (Win98; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, I untarred G98 to a system AIX 4.2 installed. Unfortunately, I don't understand UNIX deeply for I haven't use UNIX systematically before. My problem is how to run my G98 jobs on this system. G98 was installed in the directory of /usr/g98, and my home directory is /home/ybfan. Thank you very much. Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Fri Oct 29 16:22:27 1999 Received: from portal.usip.edu (portal.usip.edu [208.7.144.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA08902 for ; Fri, 29 Oct 1999 16:22:26 -0400 Received: from usip.edu by portal.usip.edu (SMI-8.6/SMI-SVR4) id QAA10782; Fri, 29 Oct 1999 16:17:52 -0400 Sender: gmoyna@usip.edu Message-ID: <381A2E74.B5D71CE@usip.edu> Date: Fri, 29 Oct 1999 16:32:04 -0700 From: Guillermo Moyna X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.5-22smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: GAMESS (Aug-99 version) and MPI... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL, I have been using GAMESS on SGI and LINUX boxes for a while now, and I really like it. In the past, I worried only about the sequential versions (in versions pre Aug-99), but now I am building a 16 node LINUX cluster and have been pondering getting both the old (pre Aug-99) and new version of GAMESS on it. I ported the old version of GAMESS to use MPI instead of TCGMSG, and it worked fine - Actually, it worked beautifully. Now, I got the new version which uses sockets, and after tinkering around a bit, I also got it to work. I did a comparison using the same input file between the old (MPI) and new (SOCKETS) versions, and I found that the MPI version was slightly faster (~ 8%) on the same network. Now, I thought I could easily compile the new version (to take advantage of the parallel MP2 calculations) using MPI instead of SCOKETS. I changet the porting in 'comp', and hacked ddi.src to look for the right mpif.h header file. It compiled seamelesly, and I got a working binary. I start it as an 'mpirun' job using 2 nodes, and I can see two mpi jobs running with ps, but the output file from GAMESS does not says anything about 2 processors, and also, the job starts only on one node. Anything huge I'm missing? BTW, I'm using the MPICH implementation of MPI, PGF77 is my compiler, my 'test' beowulf consists of 4 old pentiums. Everything works fine with MPI on the old version of GAMESS, or with sockets in the new version. Happy Hallowen! Guillermo -- +======================---------------- --- -- - - - - . | Guillermo Moyna, PhD : Department of Chemistry and Biochemistry . University of the Sciences in Philadelphia 600 South 43rd Street Philadelphia, PA 19104-4495 Phone: (215) 596-8526 - Office (215) 895-1169 - Lab Fax: (215) 596-8543 e-mail: g.moyna@usip.edu . WWW: http://tonga.usip.edu/chempage/faculty/moyna.htm : http://tonga.usip.edu/gmoyna/index.html | . - - - - -- --- ----------------======================+