From "/G=Klaus/S=Schoffel/OU=HRE/O=Norsk Hydro a.s/"@HYDRORESEARCH.telemax.no Wed Mar 17 13:15:51 1993 Date: Wed, 17 Mar 1993 12:15:51 +0100 From: "/GQ=/I=/G=Klaus/S=Schoffel/OU=HRE/O=Norsk Hydro a.s/"@hydroresearch.telemax.no Message-Id: <6442151117031993/A03909/FS1/11738ACF2900*@MHS> To: chemistry@ccl.net (Non Receipt Notification Requested) (IPM Return Requested) Subject: RS6000 IO-Performance Dear Netters, We are currently running ab initio codes on an IBM RS6000/580. A strong drawback of this machine is the poor IO performance. Our machine is configured with two SCSI-2 adaptors and 5 1.2 GB SCSI-2 disks. IO on a non-striped filesystem, located on one disk, gives a maximum through-put of ca 2Mb/s (2.9 Mb/s on a SGI 3D/35 (standard adaptor and SCSI-2 disk)). IBM claimed that running on a filesystem which is striped over 4 disks increases the IO performance to 8-10 Mb/s. Has anybody experience with striped filesystems on the IBM RS6000? Any comments are welcome Klaus Schoeffel +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + HYDRO |Klaus Schoeffel |Norsk Hydro A/S + +RESEARCH|Senior Research Scientist |Research Centre Porsgrunn + + |E-Mail: Schoffel@hydroresearch.telemax.no|P.O. 2560 + + ((( | or: SCHOEFFELK%FS.decnet@BG.HBG.HYDRO.NO|N-3901 Porsgrunn + +(=====) |Tel. : +47 3 564076 | + + |Fax : +47 3 563686 |Norway + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From ZSYAMP01@EBCESCA1.bitnet Wed Mar 17 07:22:23 1993 Message-Id: <199303171202.AA05341@oscsunb.ccl.net> Date: Wed, 17 Mar 93 11:12:13 CET From: ZSYAMP01%EBCESCA1@OHSTVMA.ACS.OHIO-STATE.EDU Subject: recording videotapes with dancing proteins? To: chemistry@ccl.net Dear colleagues, Maybe you could give me some advice on the problem I deal with at this moment. We're looking for a graphics package for the Silicon Graphics Indigo being able to MANIPULATE PROTEINS without knowing their coordinates. It is, we would like to make a sort of animation by taking initially a well-known conformation (previously computed) and then gradually, moving it as a plastic model, bending some parts, change its shape to force it to have another conformation. I don't have any computation for each one of the intermediate steps and the final geometry, so the entire process is going to be done manually, as you could do to a physical spheres-and-sticks representation of the molecule. The aim of such animation is to record a video tape to illustrate a certain theory about protein behaviour. Do you know if this is possible to accomplish now with any graphics package??? Are they so evolved??? Thanks in advance. Alicia Martinez Supercomputing Center of Catalonia BITNET: ZSYAMP01 at EBCESCA1 Internet: zsyamp01@puigmal.cesca.es From mbdtscp@hpc.ch.man.ac.uk Wed Mar 17 13:14:16 1993 From: Chris Parkinson Message-Id: <9494.9303171314@hpc.ch.man.ac.uk> Subject: MM2 for UNIX - a successful port! To: CHEMISTRY@ccl.net Date: Wed, 17 Mar 93 13:14:16 GMT _____________________ MM2 for HP-UX systems _____________________ Thank you very much for the large amount of helpful mail that I received concerning my MM2 query. It turns out that the original VAX version will compile on my HP workstations using a combination of compiler flags and a small bit of hacking! If anyone would like to know more about getting MM2 to run under the UNIX environment feel free to contact me and I'll post you my summary of editing and compiler options. __________________________________________________________________________ Chris Parkinson. Dept. of Theoretical Chemistry, Chemistry Building, Victoria University of Manchester, Manchester. M13 9PL. E-Mail: mbdtscp@mchhpc.ch.man.ac.uk __________________________________________________________________________ From ZSHI@ac.dal.ca Wed Mar 17 11:39:32 1993 Date: 17 Mar 1993 15:39:32 -0400 From: Zheng Shi Subject: Information about IBM RS6000 To: chemistry@ccl.net Message-Id: <01GVX4O60EYU000ZE0@AC.DAL.CA> Dear Netters: We are planning to buy two IBM RS6000 computers, one at top level (580) and the other lower to middle model. We will run ab initio packages most of the time. We would like to hear your advice about the system configuration, i.e. memory size, disk space and disk controllers. Also, information about workstations from other vendors would be most helpful. Thanks in advance. Zheng Shi E-Mail "ZSHI@AC.DAL.CA" Department of Chemistry Dalhousie University Halifax, Nova Scotia Canada B3H 4J3 From SVIJAYAKUMAR@EAGLE.WESLEYAN.EDU Wed Mar 17 15:40:42 1993 Date: 17-MAR-1993 14:51:32.46 From: "Dr. S. Vijayakumar" Subject: lpd To: chemistry@ccl.net Message-Id: <01GVX34Z9FF48WWA02@EAGLE.WESLEYAN.EDU> Hi: I would like to know if anyone is aware of any public domain (preferable) and/or commercial line printer daemons (lpd) that can run on an IBM PC/clone that can support printer queues that are both UNIX and VMS compatible. Essentially, we are looking for some software that would allow us to print on a post script printer attached to a PC (that's on ethernet) from a remote workstation. Please respond directly to me and I will summarize for the net if there's sufficient interest. Thank you. Vijay ************************************************************************* * S. Vijayakumar * * Department of Chemistry * * Wesleyan University * * Middletown, CT 06459. * * Voice : (203) 347-9411, x3111 * * Fax : (203) 344-7960 * ************************************************************************* From ZSHI@ac.dal.ca Wed Mar 17 12:58:48 1993 Date: 17 Mar 1993 13:58:36 -0400 From: ZSHI@ac.dal.ca Subject: Information about IBM RS6000 To: chemistry@ccl.net Message-Id: <01GVX13FLUVM000S9B@AC.DAL.CA> Dear Netters: We are planning to buy two IBM RS6000 computers, one at top level (580) and the other lower to middle model. We will run ab initio packages most of the time. We would like to hear your advice about the system configuration, i.e. memory size, disk space and disk controllers. Also, information about workstations from other vendors would be most helpful. Thanks in advance. Zheng Shi E-Mail "ZSHI@AC.DAL.CA" Department of Chemistry Dalhousie University Halifax, Nova Scotia Canada B3H 4J3 From srheller@asrr.arsusda.gov Wed Mar 17 12:18:00 1993 Message-Id: <199303172123.AA15839@oscsunb.ccl.net> Date: 17 Mar 93 16:18:00 EDT From: "STEPHEN R. HELLER" Subject: Software for review To: "chemistry" 17 March, 1993 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I now have some packages in hand (see below) and I am looking for people who are willing to review the software. In return for the review you get to keep the software. The review should be completed in 1-2 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. I have tried this approach with some software for review in the past few months and it is working reasonably well. (For those who haven't finished your reviews of software sent a few months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I hope it continues to work. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 20 March, as I am sure the software will be gone by then. I can be reached on INTERNET (SRHELLER@ASRR.ARSUSDA.GOV), or if necessary, by phone at 301-504-6055 or FAX at 301-946-2704. PLEASE BE SURE TO INCLUDE AN STREET ADDRESS AND PHONE NUMBER!!! (I send the software by Federal Express.) Steve Heller The packages I now have are: 1. CSC ChemOffice from Cambridge Scientific. A Mac based drawing, modeling, and Information Management package. The software "seamlessly" integrate chemical structure drawing, molecular modeling, and information management. 2 & 3. Chapman & Hall CD-ROM versions of their Natural Products (version 1.2) and Dictionary of Organic Compounds (version 1.1). These run on an IBM PC and require a CD-ROM. According to the agreement from the company, it will be necessary to sign a license agreement with Chapman & Hall, but you will be able to keep the CD-ROM - a feature not available to paying customers of the system. 4. ChemWindow for the IBM PC running under Windows & ChemIntosh for the Mac. This is a very popular chemistry drawing program. 5. IBM PC version of the Mass Spectrometry Bulletin. This is said to be a new and improved version of the software and database. 6. MLAB, a Mathematical Modeling Laboratory package, for the IBM PC from Creative Software. This is a program for mathematical and statistical modeling based on a NIH mainframe program developed in the 1970's and enhanced since then on a regular basis. 7. Wordperfect "Presentations", version 2.0 for the IBM PC/DOS. From mlorenz@ecn.purdue.edu Wed Mar 17 15:20:24 1993 Date: Wed, 17 Mar 93 20:20:24 -0500 From: mlorenz@ecn.purdue.edu (Michael Lorenz) Message-Id: <9303180120.AA04709@cn.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: MOPAC: Opt. TS Just want to thank everyone for all of the suggestions. It was very helpful. Thanks, Mike Lorenz From urquhart@mcmail.cis.mcmaster.ca Wed Mar 17 16:29:12 1993 Date: Wed, 17 Mar 1993 21:29:12 -0500 (EST) From: stephen urquhart Subject: Re: Software for review To: "STEPHEN R. HELLER" Message-Id: I am interested. I will edit out the lines below to leave the packages that I am qualified to examine. Stephen Urquhart Department of Chemistry McMaster University 1280 Main Street West Hamilton, Ontario L8S 4M1 (416)-525-9140 x4864 Stephen Urquhart urquhart@mcmail.cis.mcmaster.ca Home 416-547-7647 Work 416-525-9140 x4864 > > 4. ChemWindow for the IBM PC running under Windows & ChemIntosh > for the Mac. This is a very popular chemistry drawing program. > > 6. MLAB, a Mathematical Modeling Laboratory package, for the IBM > PC from Creative Software. This is a program for mathematical > and statistical modeling based on a NIH mainframe program > developed in the 1970's and enhanced since then on a regular > basis. > > 7. Wordperfect "Presentations", version 2.0 for the IBM PC/DOS. > > As our lab has a variety of computers (at least one of each of XT, 286, 386 and 486) with different configurations, I would be able to test the use of these programs on different platforms and memory configurations and amounts. The later critereon is perhaps the most important in this comparison, as it seems that windows memory requirements are always underinflated. Cheers, Stephen