From chemistry-request@server.ccl.net Fri Mar 21 09:18:29 2003 Received: from f1n1.spenet.wfu.edu ([152.17.8.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2LEITr31612 for ; Fri, 21 Mar 2003 09:18:29 -0500 Received: from wfu.edu (swofford.computer.wfu.edu [152.17.95.72]) by f1n1.spenet.wfu.edu (8.11.6/8.11.6) with ESMTP id h2LEIJU112128 for ; Fri, 21 Mar 2003 09:18:19 -0500 Message-ID: <3E7B1F27.1020106@wfu.edu> Date: Fri, 21 Mar 2003 09:18:15 -0500 From: Robert Swofford Organization: Wake Forest University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en,zh-TW,zh-CN,zh,ja,ko,tr,ru MIME-Version: 1.0 To: CCL Listserv Subject: Multiprocessor scheduling G98/Linda on a Linux cluster Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit We have a new Beowulf cluster and have recently installed Gaussian98 with the Linda parallel-processing utilities. If I understand correctly, the installed version of G98 (g98L?) recognizes when it's running on a cluster, and if requested, will execute the parallelized sections of the code on multiple processors. I see in the Link 0 section of the g98 input a variable, %NProc=N, which requests multiple processors (it's also available in default.route). What I don't understand is how the batch scheduler sets aside the needed processors and identifies them to g98. We are running the portable batch scheduler (OpenPBS) with the Maui scheduler instead of the default OpenPBS FIFO scehduler. Do I just tell PBS the number of nodes to reserve? I can't see how that information gets from the scheduler to g98. Please respond off-list, and I will summarize for the list. Can someone who is running g98/Linda on a similar system share with me your batch script and perhaps clear up my confusion? I hesitate to dig into the code when I know that others have figured this out! Thanks in advance for your help! Bob Swofford -- Robert L. Swofford Professor of Chemistry Wake Forest University Winston-Salem, NC 27109-7486 swofford@wfu.edu http://www.wfu.edu/~swofford/ (336)-758-4490 Telephone (336)-758-4656 FAX From chemistry-request@server.ccl.net Fri Mar 21 08:31:12 2003 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2LDVBr30634 for ; Fri, 21 Mar 2003 08:31:11 -0500 Received: from health.nb.ca ([10.10.94.100]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-58282U90000L90000S0V35) with ESMTP id ca for ; Fri, 21 Mar 2003 09:31:10 -0400 Message-ID: <3E7B132E.3050004@health.nb.ca> Date: Fri, 21 Mar 2003 09:27:10 -0400 From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en MIME-Version: 1.0 To: ccl Subject: protein folding Content-Type: multipart/alternative; boundary="------------020907000906030006070806" --------------020907000906030006070806 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All, I need an advice. I am trying to get some functional information about several proteins with only primary structures known and (at least for most parts) without similarity with any proteins with known 3d structure. So I am trying to use predicted structures from bioinformatics ab initio methods. The question is: in your opinion should I further energy minimize obtained 3D structure of a protein backbone or would that just ruin statistical prediction. Any experiences, ideas, hints or references would be appreciated All the best Mira - --------------020907000906030006070806 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All,
I need an advice. I am trying to get some functional information about several proteins with only primary structures known and (at least for most parts) without similarity with any proteins with known 3d structure. So I am trying to use predicted structures from bioinformatics ab initio methods. The question is: in your opinion should I further energy minimize obtained 3D structure of a protein backbone or would that just ruin statistical prediction.
Any experiences, ideas, hints or references would be appreciated
All the best
Mira

--------------020907000906030006070806-- From chemistry-request@server.ccl.net Fri Mar 21 12:06:03 2003 Received: from mail.ic.sunysb.edu ([129.49.1.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2LH62r03278 for ; Fri, 21 Mar 2003 12:06:03 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.8/8.12.8) with SMTP id h2LH5xPK003345 for ; Fri, 21 Mar 2003 12:06:02 -0500 (EST) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (NAVGW 2.5.2.9) with SMTP id M2003032112060223799 ; Fri, 21 Mar 2003 12:06:02 -0500 Received: from sparky.ic.sunysb.edu (sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.8/8.12.8) with ESMTP id h2LH62Sc003360; Fri, 21 Mar 2003 12:06:02 -0500 (EST) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.8/8.12.8) with ESMTP id h2LH62lc015034; Fri, 21 Mar 2003 12:06:02 -0500 (EST) Date: Fri, 21 Mar 2003 12:06:02 -0500 (EST) From: Yong Liang Yang To: jkl@ccl.net cc: chemistry@ccl.net Subject: .mmod and .dat file Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all: I am trying to run a minimization job in Batch mode using Macromodel program. My input files are .mmod files (from Catalyst program) which contain the information for all of the conformations for one single molecule. But the .mmod file can not be run in Batch mode in Macromodel (can be run in interactive mode) As manual says,the input file type for batch mode should be .dat file,which seems contain the information only for one conformation for one molecule. Does anybody knows how to convert the .mmod file into .dat file or how to run the .mmod file in Batch mode? Many thanks in advance! YL. Yang SUNY-Stony Brook 631-632-5796 From chemistry-request@server.ccl.net Fri Mar 21 18:18:12 2003 Received: from adenine.cgl.ucsf.edu ([169.230.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2LNICr12011 for ; Fri, 21 Mar 2003 18:18:12 -0500 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.8/8.12.8/GSC1.16) with ESMTP id h2LNICVO943343 for ; Fri, 21 Mar 2003 15:18:12 -0800 (PST) Date: Fri, 21 Mar 2003 15:18:12 -0800 (PST) From: Pradipta Bandyopadhyay To: chemistry@ccl.net Subject: spherical harmonics! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am looking for regular spherical harmonics in cartesians for L > 4 ( The book by A. J. Stone - the theory of intermolecular forces has until L=4, page 227). Can anyone help me with this? thanks. Pradipta