From MURASHOV@chem1.chem.dal.ca Mon May 23 08:56:45 1994 Received: from Snoopy.UCIS.Dal.CA for MURASHOV@chem1.chem.dal.ca by www.ccl.net (8.6.4/930601.1506) id IAA29700; Mon, 23 May 1994 08:55:35 -0400 Received: from chem1.chem.dal.ca (CHEM1.Chem.Dal.Ca [129.173.17.47]) by Snoopy.UCIS.Dal.CA (8.6.8.1/8.6.6) with SMTP id JAA21986 for ; Mon, 23 May 1994 09:55:33 -0300 Message-Id: <199405231255.JAA21986@Snoopy.UCIS.Dal.CA> Received: from CHEM1/MERCURYQUEUE by chem1.chem.dal.ca (Mercury 1.1); Mon, 23 May 94 9:55:33 -0400 From: "MURASHOV VLADIMIR" To: chemistry@ccl.net Date: Mon, 23 May 1994 09:55:02 AST Subject: MD potentials Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Dear netters, Does somebody know some sort of a list or a data base where interatomic potential parameters (Buckingham or B-H-M models) suitable for MD simulation of solids are collected? Any suggestions will be appreciated. Thank you very much, Best regards, Vladimir. Dalhousie University, Halifax, NS Canada. From calzado@quantix.us.es Mon May 23 09:56:52 1994 Received: from quantix.us.es for calzado@quantix.us.es by www.ccl.net (8.6.4/930601.1506) id JAA00415; Mon, 23 May 1994 09:55:07 -0400 Received: by quantix.us.es (AIX 3.2/UCB 5.64/4.03) id AA12518; Mon, 23 May 1994 15:53:40 +0100 Date: Mon, 23 May 1994 15:53:40 +0100 From: calzado@quantix.us.es (Carmen Jimenez Calzado) Message-Id: <9405231453.AA12518@quantix.us.es> To: CHEMISTRY@ccl.net Subject: crystallographic data basis Dear netters, Does somebody know some public domain data basis where crystallographic data of solids (angles,axial lengths,...) are collected? I'm looking for crystallographic data of [Cu2Cl2][NEt4] Any suggestions will be appreciated. Thank you very much, Best regards, Carmen. ------------------------------------ Carmen Jimenez Calzado Ph. D. Student e-mail:calzado@quantix.us.es Departamento de Quimica Fisica Facultad de Quimicas. Universidad de Sevilla. Spain ------------------------------------ From toukie@zui.unizh.ch Mon May 23 09:59:52 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.4/930601.1506) id JAA00193; Mon, 23 May 1994 09:28:02 -0400 Received: from rzurs5.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA21983; Mon, 23 May 94 15:28:01 +0200 Received: by rzurs5.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA25355; Mon, 23 May 1994 15:28:00 +0200 From: toukie@zui.unizh.ch (Hr Dr. S. Shapiro) Message-Id: <9405231328.AA25355@rzurs5.unizh.ch> Subject: Location of certain subdirectories and files To: chemistry@ccl.net Date: Mon, 23 May 1994 15:28:00 +0100 (MEST) X-Mailer: ELM [version 2.4 PL13] Content-Type: text Content-Length: 823 To whom it may concern: I read in a recent posting of a file named "fit-any-function" that was supposed to be in ftp.ccl.net /pub/chemistry/software. However, I was unable to locate this file. How do I access it? When I went into ftp.ccl.net /pub/chemistry/software I found a subdirectory called "MS-WINDOWS". When I opened this subdirectory I saw another subdirectory called "Titration_simul_for_Winds". However, when I typed cd Titration_simul_for_Winds I got a message: No such file or directory How do I access the subdirectory "Titration_simul_for_Winds"? Thanks in advance for your help. Sincerely, S. Shapiro Internet: toukie@zui.unizh.ch From hogue@canada.den.mmc.com Mon May 23 10:56:51 1994 Received: from canada.den.mmc.com for hogue@canada.den.mmc.com by www.ccl.net (8.6.4/930601.1506) id KAA00580; Mon, 23 May 1994 10:00:39 -0400 Received: by canada.den.mmc.com (4.1/1.34.a) id AA01855; Mon, 23 May 94 08:00:06 MDT Date: Mon, 23 May 94 08:00:06 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9405231400.AA01855@canada.den.mmc.com> To: chemistry@ccl.net Subject: error in acetal function I made an error in the acetal function of model perfluoropolyether shown by Hyperchem to participate in the LUMO, it shpould be -(O-CF2-O)-. Pat Hogue From jkl@ccl.net Mon May 23 10:57:53 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id KAA01103; Mon, 23 May 1994 10:31:37 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id KAA09836; Mon, 23 May 1994 10:31:34 -0400 Date: Mon, 23 May 1994 10:31:34 -0400 Message-Id: <199405231431.KAA09836@krakow.ccl.net> To: toukie@zui.unizh.ch Subject: Re: Location of certain subdirectories and files In-Reply-To: Mail from 'toukie@zui.unizh.ch (Hr Dr. S. Shapiro)' dated: Mon, 23 May 1994 15:28:00 +0100 (MEST) Cc: jkl@ccl.net, chemistry@ccl.net Dear Dr. S. Shapiro, I am in the process of rearranging CCL software archives on www.ccl.net The software directory is now organized by platform/language rather than as a flat directory of programs. In the case of fit-any-function, its location now is: /pub/chemistry/software/SOURCES/FORTRAN/fit-any-function Before I create appropriate README/INDEX files, you need to retrieve the /pub/chemistry/software/ls-lR file to find what is where. As to: Titration_simul_for_Winds, you are using some strange blend of ftp, which cuts the portion of the file name or has some limits on file name length. The program is located in: /pub/chemistry/software/MS-WINDOWS/Titration_simul_for_Windows For some reason, your ftp allows only names shorter than 25 characters. While I will make the names shorter in some future, It can be done when I have INDEXEs for files ready. And with my current load, it will not be tomorrow. Jan jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From cmartin@rainbow.uchicago.edu Mon May 23 11:56:53 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id LAA01905; Mon, 23 May 1994 11:26:20 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Mon, 23 May 94 10:26:19 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA07571; Mon, 23 May 94 11:07:19 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9405231607.AA07571@rainbow.uchicago.edu> Subject: Computing Bond Strengths To: chemistry@ccl.net Date: Mon, 23 May 1994 11:07:18 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1386 There has been some discussion about computing bond stregnths, and I am wondering if anyone has tried or has some thought about the following: Using ab initio calculations, one can compute absolute energies with a high level correlated calculation, like Hartree Fock plus perturbation theory (MP2, MP4, etc.) Clearly one can calculate dissociation energies just by strecthing the bond. On the other hand, I can imagine reformulating the MP2/MP4 equations so that the bond energies woulod appear directly. For example, recently papers have appeared by Aml\"of (Chemical Physics Letters, 1991 or 1992, I think) that describe reformulating the MP2/MP3/... equations using a loclaized basis. I believe that the intetnt of these papers was to simply speed up the MP2 computation, but I think that accurate bond energies could also be computed if the energy compoents could be cleanly seperated into bond terms, bond-bond interactions, etc. ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From Jorge.Medrano@UC.Edu Mon May 23 11:58:13 1994 Received: from ROCK.SAN.UC.EDU for Jorge.Medrano@UC.Edu by www.ccl.net (8.6.4/930601.1506) id LAA01856; Mon, 23 May 1994 11:20:08 -0400 From: Received: from UCBEH.SAN.UC.EDU by UCBEH.SAN.UC.EDU (PMDF V4.3-8 #4918) id <01HCOC64EUB49892CF@UCBEH.SAN.UC.EDU>; Mon, 23 May 1994 11:12:52 EST Date: Mon, 23 May 1994 11:12:51 -0500 (EST) Subject: Bond strenghts To: chemistry@ccl.net Message-id: <01HCOC64F3YA9892CF@UCBEH.SAN.UC.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear co-neters: P. S. Subranian asks about how to calculate "bond strengths" There are not many theories that give a rigorous way to calculate bond strengths in an unambiguous way. Dissociation energies are, in my opinion, a very different thing. There is however a rigorous formalism that yields "degrees of bonding", using only the density matrix, and doesn't need to use any arbitrarily defined integration volume. This formalism allows the calculation of the degrees of bonding for a closed-shell; open-shell (UHF or ROHF) with or without CI, wavefunction. It can even be used with a periodic-boundary conditions (for infinite systems) wavefunction. See for instance: J. Medrano et al., Phys Rev. B, 40, 7186 (1989) or J. Medrano et al., Theochem 200, 463 (1989) or J. medrano et al., J. Phys. B 26, 827 (1993) and the references in those papers. The formalism calculates also other useful quantities, like active charge, etc; and in the case of an open shell system can be used to calculate the partition of spin density. In fact, the theory is a rigorization and extension of the algorithm proposed originally by Armstrong, Perkins and Stewart (J.Chem. Trans. Dalton 838 (1973), with which it agrees for a closed shell system. The full thing is implemented in MOPAC93, but former versions of MOPAC provide the results that the original algorithm yields. Caution: the original algorithm will not give the correct results for systems other than closed-shell. In any case, there is an important advantage to this kind of calculation, whether with the original or the extended formalism. It gives 1.0 (or very close to) for the degree of bonding of a "classical single bond" (standard closed shell system), very close to 2.0 for a double bond and 3.0 for a triple bond. TYhis is of course not imposed, it reults from the calculation. for systems other than closed shell, the theory gives a natural extension of the classical notion of bond, in a quite rigorous fashion. I hope this helps. Jorge Medrano medrang@ucbeh.san.uc.edu From YUAN@UCCHEM.OA.UC.EDU Mon May 23 12:56:56 1994 Received: from UCCHEM.OA.UC.EDU for YUAN@UCCHEM.OA.UC.EDU by www.ccl.net (8.6.4/930601.1506) id MAA02805; Mon, 23 May 1994 12:40:20 -0400 Date: Mon, 23 May 1994 12:39:36 EDT From: YUAN@UCCHEM.OA.UC.EDU (JieYuan,Chemistry,U.Cincinnati) Message-Id: <940523123936.1a9d@UCCHEM.OA.UC.EDU> Subject: CSD at NCI on VAX - up dated 04/94 To: chemistry@ccl.net X-Vmsmail-To: SMTP%"chemistry@ccl.net" Dear Netters: I found that the CSD (Cambridge Structural Database) on the NCI (National Cancer Institute) Supercomputer Center's VAX is an up to date version! In case you don't know, the CSD on OSC's Cray is an out of date version. New version for Cray is still under development. If you have account on the NCI's VAX cluster, you can do searches yourself. The procedures are similar to the Cray version, only more easily and userfriendly. Cheers! 5/23/94 ===== Jie Yuan === Chemistry === U. Cincinnati === Jie.Yuan@UC.EDU ===== From FLEMMING@dfhvax.nbi.dk Mon May 23 12:57:59 1994 Received: from nbivax.nbi.dk for FLEMMING@dfhvax.nbi.dk by www.ccl.net (8.6.4/930601.1506) id MAA02604; Mon, 23 May 1994 12:17:12 -0400 From: Received: from DECNET-MAIL (FLEMMING@DFHVAX) by nbivax.nbi.dk (PMDF V4.2-13 #5783) id <01HCOS1ZW8SGC8SZ0W@nbivax.nbi.dk>; Mon, 23 May 1994 18:17:09 +0200 Date: Mon, 23 May 1994 18:17:09 +0200 Subject: electron density maps --> SYBYL To: chemistry@ccl.net Message-id: <01HCOS1ZX1QAC8SZ0W@nbivax.nbi.dk> X-VMS-To: FLEMMING, CCL MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, We are going to run a course on "Advanced Structural Chemistry and Molecular Modelling" for our Ph.D. students within a couple of weeks. One of the exercises we plan to have on the course is to build an inhibitor into the electron density map determined by X-ray crystallography. For practical purposes, we are only using the SYBYL software for all the exercises, including the above one. Does anyone have a program which converts an electron density map generated by CCP4, PHASES or XPLOR into a SYBYL contour map ? I'm aware that Tripos together with SYBYL distribute some fortran programs to help doing the conversion, but they only takes me half of the way (the last half). I would be very grateful, if anyone could help me. In advance thank you. Flemming flemming@dfhvax.nbi.dk ********************************************** * * * Flemming Steen Jorgensen * * Associate professor, Ph.D. * * * * Royal Danish School of Pharmacy * * Department of Medicinal Chemistry * * Universitetsparken 2 * * DK-2100 Copenhagen * * Denmark * * * * Phone: +45 35 37 08 50 ext. 378 * * Fax: +45 35 37 22 09 * * E-mail: flemming@dfhvax.nbi.dk * * * ********************************************** From fant@rocketman.ncifcrf.gov Mon May 23 13:56:57 1994 Received: from fcs280s.ncifcrf.gov for fant@rocketman.ncifcrf.gov by www.ccl.net (8.6.4/930601.1506) id NAA03518; Mon, 23 May 1994 13:25:39 -0400 Received: from rocketman.ncifcrf.gov by fcs280s.ncifcrf.gov (4.1/NCIFCRF-3.0/AWF-2.0) id AA11420; Mon, 23 May 94 13:15:31 EDT Received: by rocketman.ncifcrf.gov (920330.SGI/911001.SGI) for @fcs280s.NCIFCRF.GOV:chemistry@ccl.net id AA04208; Mon, 23 May 94 13:24:19 -0400 From: fant@rocketman.ncifcrf.gov (Andrew D. Fant) Message-Id: <9405231724.AA04208@rocketman.ncifcrf.gov> Subject: Re: CCL:CSD at NCI on VAX - up dated 04/94 To: YUAN@UCCHEM.OA.UC.EDU (JieYuan Chemistry U.Cincinnati) Date: Mon, 23 May 1994 13:24:18 -0400 (EDT) Cc: chemistry@ccl.net In-Reply-To: <940523123936.1a9d@UCCHEM.OA.UC.EDU> from "JieYuan,Chemistry,U.Cincinnati" at May 23, 94 12:39:36 pm X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1170 Hello all, As the person responsible for the CSD at the NCI FCRF Biomedical Supercomputer Center, I would like to just expand and clarify on the status of it here. We have the current versions availible not only on our vaxen, but also on the sun and sgi workstation clusters. If you are using our site, I would advise against using it from the cray or the vaxen. Your best bet for performance is to access it from one of the SGI servers, which will give you the best disk performance and support for the quest-3D menus. My apologies if this is not of general interest, but I wanted to cover all the bases about the software. If there are people who are interested in access to our site, please contact me in email, and I would be glad to provide more information about access policies and the like. For what it's worth, Andy -- Andrew D. Fant Applications Analyst fant@ncifcrf.gov NCI-Frederick Cancer Research Facility Biomedical Supercomuting Center (301)846-5764 Me?!? Have an official NCI or Dyncorp Opinion? HAH! "I'm just one too many mornings and a thousand miles behind" -- B. Dylan From mizan@engin.umich.edu Mon May 23 15:56:54 1994 Received: from rz.engin.umich.edu for mizan@engin.umich.edu by www.ccl.net (8.6.4/930601.1506) id PAA04990; Mon, 23 May 1994 15:09:41 -0400 Received: (mizan@localhost) by rz.engin.umich.edu (8.6.8/8.6.4) id PAA25317 for CHEMISTRY@ccl.net; Mon, 23 May 1994 15:09:40 -0400 Date: Mon, 23 May 1994 15:09:40 -0400 From: "Tahmid I. Mizan" Message-Id: <199405231909.PAA25317@rz.engin.umich.edu> To: CHEMISTRY@ccl.net Subject: Summary on HP vs SUN machines for MD SUMMMARY OF RESPONSES TO QUERY ON HP AND SUN WORKSTATIONS Original question: ================= > Hi Netters, > I am considering buying one of the following workstations: > 1) HP model 712/60 32MB main memory 60MHz PA-RISC7100LC processor > 2) SUN SPARCSTATION 20 model 50 32MB main memory 50 MHz supersparc processor > I will be using the workstations primarily for MD simulations. > Does anyone have any ideas about how these machines compare in terms of > speed and ability to load large programs (large memory requirements) ? > > I would appreciate comments, experience, anecdotes etc. ****************************************************************************** From: eloranta@kala.cc.jyu.fi (Jussi Eloranta) I think that the main differences are: 1) HP is probably faster using single CPU (esp. on floating point). 2) Sun SS20 can be expandet to multiple CPUs. MD simulations parallelize so it can take advantage of multiple cpus (if you want to expand your sys). 3) Sun has more commercial stuff available than HP. (for example, we run SYBYL on our Sparc 10 which is not available for HP). 4) Sun is in progress of changing its operating system from BSD to SVR4 based. Solaris 2.3 is not very stabile without patches, but works ok with approriate patches. Solaris 2.4 is supposedly ok. HP has been using its current op. sys. (HPUX) for long time, so it may be more stabile. BTW HPUX is not SVR4 - it's somewhere between SVR3 and BSD.... HP is faster on FP and sun probably on int. I think both systems come with fast SCSI II disks, so there shouldn't be very big differences. Also make sure that your local HP or Sun software support is OK. I mean that they actually will be able to help you if something happens... Regards, Jussi ****************************************************************************** From: "'Arne Elofsson (arne@hodgkin.mbi.ucla.edu)'" We did a lot of MD-testing (CHarmm) on different maschines a few years ago and SUN never compared efficiently in Speed/$. We had problems compiling on HP and ended up bying IBM RS/6000:s (in 1991-92) and Dec alphas lately. arne ****************************************************************************** From: "Arne Elofsson (arne@hodgkin.mbi.ucla.edu)" Subject: Re: clarification on hp compiler This was in 1990/91 and the charmm just did not run. But i know it works fine now. I have no experience with HP. yours arne ****************************************************************************** From: vijaya@chem.psu.edu Hi We also do MD simulations mainly in our group. We are in the process of obtain some new computers. We already have one HP 700 series. There is no doubt it did quite well in the last two years. But for the new one that we plan to buy we choose SUN SPARCSTATION. The new SPARCs have got two processors and if you have two jobs running you will really appreaciate the performance. But for memory most of the things dont require more than 32MB, however if you can upgrade it to 64MD (MB) you will be comfortable. Before buying you can always do some test runs on their machines I guess. That's what we did atleast. vijaya@chem.psu.edu ****************************************************************************** From: Dan Severance I don't have any experience with the SparcStation 20, nor the HP 712. My general experience with the SUN line, though, is that the SpecMarks overestimate the actual performance of SUNs for Monte Carlo and Dynamics codes, especially using explicit solvent. The HP 735/99 is the fastest machine I've tested for Dynamics, (2x and SGI R4400 Indy, the second fastest machine that I've tested), but I don't know the relative speed of the 712 to the 735. I've tested IBM (disappointing), SUN (slow), SGI, and HP machines, along with the DEC Alpha (disappointing). The SGI machines I tested were less than half the price of an HP 735, so the price/performance was similar for both, with SGI getting the edge due to a more robust OS with fewer nasty porting problems. The HP compilers tend to be flaky, with code running fine on one version and dying on the next. That's my $0.02; I'd be interested in knowing if SUN has gotten their act together on the newer machine, but from what I've read they are concentrating too much on business (raw speed not so important) and not enough on science. Dan Severance dan@omega.chem.yale.edu P.S. In the past, the SUNs have had more difficulty with memory management, again I don't know if they've addressed that at all. ****************************************************************************** From: Dan Severance Subject: Re: clarification on hp compiler In the past they haven't had things like getarg (admittedly not a STANDARD fortran item, but every UNIX platform I have worked on has had it (AMBER(md) uses it, as does BOSS(MC)). They do have an IGETARG function and now I think may have added the getarg. ****************************************************************************** From: Dan Severance I just talked to the people who have a number of HPs, and they have a 712 on demo loan. They like it a lot, and tell me that it's about 20% faster than an SGI R4000 machine, for about the same price. The HPs have a reasonably good X-windows graphics system (fast). I'd say go with the HP (assuming you don't need to run any GL graphics programs, HP has no plans to support OpenGL). Dan ****************************************************************************** From: "Ian Dillon" Dr. Mizan Have you also considered a Silicon Graphics workstation? We have a very strong pressence in the computational chemistry arena and the INDY/Indigo2 product line would serve you very well (both from a CPU and graphics perspective). If you are interested in either of these pro- ducts, please reply with your mailing address and phone number. Thanks, -- Ian Dillon Systems Engineer Email: dillon@indianapolis.sgi.com Silicon Graphics, Inc. Phone: 317-595-6363 FAX: 317-595-6360 ****************************************************************************** From: afj@chem.ucla.edu (Andy Jacobson) About the workstations, I can tell you that there is a long standing bug in the malloc in HPUX that will not allow the machine to access swap space past the default swap partition. This was a real killer when we tried running AVS on an HP715 demo we had, as the software (commercial) was compiled without using one or another of the special lib mallocs available. I would suggest that if you have a demo machine, make sure all the binaries you use are compiled to get past this problem, (create additional swap partitions, and test with large array). The sun has no such problem, though it is my feeling that it is the worse of the two machines you are considering. The HP's have very good performance when it comes to number crunching. -A.J. ****************************************************************************** ************************************************************************ *********************************************************************** Tahmid Mizan University of Michigan From KUS@SUEARN2.bitnet Mon May 23 14:00:49 1994 Received: from unic.uni-c.dk for KUS@SUEARN2.bitnet by www.ccl.net (8.6.4/930601.1506) id NAA03713; Mon, 23 May 1994 13:54:44 -0400 Received: from ncc.free.net by unic.uni-c.dk (5.67b+/1.34) id AA07827; Mon, 23 May 1994 19:53:58 +0200 Received: from univax.free.net by ncc.free.net with SMTP id AA00362 (5.65c8/EM.01/IDA-1.4.4 for CHEMISTRY@ccl.net); Mon, 23 May 1994 17:49:56 GMT Message-Id: <199405231749.AA00362@ncc.free.net> Received: from SUEARN2.BITNET (MAILER) by RUUNICOM (MX V3.3 VAX) with BSMTP; Mon, 23 May 1994 21:50:38 +0400 Date: Mon, 23 May 94 21:49 MSK To: CHEMISTRY@ccl.net From: Mikhail Kuzminsky (095)-135-6388 Subject: CCL:SUN vs HP workstations X-Russian: Cyrillic > I am considering buying one of the following workstations: > > 1) HP model 712/60 32MB main memory 60MHz PA-RISC7100LC processor > 2) SUN SPARCSTATION 20 model 50 32MB main memory 50 MHz supersparc processor > > I will be using the workstations primarily for MD simulations. > > Does anyone have any ideas about how these machines compare in terms of > speed and ability to load large programs (large memory requirements) ? First of all you may take into account usual benchmarks data as SPECint, SPECfp and LINPACK MFLOPS. There are: workstation SPECint92 SPECfp92 HP9000 712/60 58 79 SUNstation 20 mdl 50 69,2 78,3 (I don't have LINPACK data near me :-( ). But this data is only first approximation to estimation of performance of MD programs. If the MD benchmarks for this workstation are unavailable for you, you may receive a bit more good approximation on the following way : 1) Take the benchmark MD data for another models of SUN (SUN station 10 for example) and HP 2) Re-calculate this data on the base of performance relations betweeen for example SUN station 10 model 50 and SUN station 20 model 50. Mikhail Kuzminsky, N.D.Zelinsky Institute of Organic Chemistry,Moscow. PS. I may recommend to take into account DEC3000 ALPHA AXP mdl 300LX or mdl 300X which are also very good in the sense of price/performance relationship and which have performance relative close to workstations you are estimating. From jkl@ccl.net Mon May 23 16:56:50 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id QAA06222; Mon, 23 May 1994 16:54:29 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id QAA10048; Mon, 23 May 1994 16:54:28 -0400 Date: Mon, 23 May 1994 16:54:28 -0400 Message-Id: <199405232054.QAA10048@krakow.ccl.net> To: chemistry@ccl.net Subject: security WHOLE on AIX sustem Cc: jkl@ccl.net Dear Netters, Pedro Vazquez ask me to point to an important security hole in the AIX (RS6000 UNIX). Simply stated, you can log in to any account on RS6000 machine (but I will not tell you how...). Most of you know about it, but just in case... The way to fix the bug is: A fix for this rlogind problem can be found on anon.ftp. software.watson.ibm.com:/pub/rlogin/rlogin.tar.Z -rw-r--r-- 1 root 0 323659 May 21 01:57 rlogin.tar.Z You can also contact your friendly IBM representative. Jan jkl@ccl.net From C1790@SLVAXA.UMSL.EDU Mon May 23 17:58:06 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id RAA07930; Mon, 23 May 1994 17:45:15 -0400 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HCOOYYZB1YCWH60O@SLVAXA.UMSL.EDU>; Mon, 23 May 1994 16:47:53 CST Date: Mon, 23 May 1994 16:47:53 -0600 (CST) Subject: SUMMARY ON A CENTRAL RESOURCE FOR COMPUT. CHEM. VIDEOS To: CHEMISTRY@ccl.net Message-id: <01HCOOYYZKP4CWH60O@SLVAXA.UMSL.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT DEAR NETTERS, SOME TIME AGO I REQUESTED INFORMATION AS TO A CENTRAL RESOURCE FOR VIDEOS, ETC., ON COMPUTATIONAL CHEMISTRY. HERE IS THE SUMMARY OF RESPONSES. BEST REGARDS. .... BILL WELSH DEPT. OF CHEMISTRY UNIV. OF MISSOURI-ST. LOUIS Bill Welsh, I was employed as a consultant to help generate the date for a Fujitsu promotional video. I used AVS and displayed three decarbonylation reactions. I had structure change as well as the change in HOMO displayed. The video ended up to be quite neat. It was a fair bit of work though! regards, Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University canberra, ACT, Australia There is a liitle bit of this at the NIH Guide to Molecular Modelling WWW home page (http://www.nih.gov/molecular_modeling/techniques.html) and an animation in Henry Rzepa's electronic manuscript ( locate through http://www.ch.ic.ac.uk) Cheers, Dave _______________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. Hi, I saw your msg at COMP-CHEM. Here, in Brazil, I am developping scientific educations software. If you want to see, please, ask me, ok ? Sincerely yours, Fernando Luis --------------------------------------------------------------------------- Fernando Luis Barroso da Silva Departamento de Quimica - Faculdade de Ciencias Universidade Estadual Paulista - UNESP 10-54, Julio de Mesquita Filho St. Zip Code: 17044-450 - City: Bauru/SP - Country: BRAZIL email: flbdsilv@fox.cc.usp.br Phone: +55 0142 30-2111 - R. 134 Fax: +55 0142 30-4470 ---------------------------------------------------------------------------- From C1790@SLVAXA.UMSL.EDU Mon May 23 18:01:57 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id RAA07914; Mon, 23 May 1994 17:44:32 -0400 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HCOOY0XKW0CWH60O@SLVAXA.UMSL.EDU>; Mon, 23 May 1994 16:47:07 CST Date: Mon, 23 May 1994 16:47:07 -0600 (CST) Subject: SUMMARY ON PREDICTING pKa's To: CHEMISTRY@ccl.net Message-id: <01HCOOY0YNGYCWH60O@SLVAXA.UMSL.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT DEAR NETTERS, SOME TIME AGO I REQUESTED INFO. ON PREDICTING THE pKa's OF ORGANICS. HERE'S THE SUMMARY OF RESPONSES ... BILL WELSH DEPT. OF CHEMISTRY UNIV. OF MISSOURI-ST. LOUIS Bill, I don't know if it what you had in mind, but there are two computational methods for calculating pKa's for proteins. See: Bashford et al. (1993) Biochem 32, 8045. and Yang et al. (1993) Proteins 15, 252-265. Hope this helps. Rob Setlik Biophysics Dept. Roswell Park Cancer Inst. Buffalo, N.Y. 14263 Dear Dr. Welsh (and prospective others); An excellent programme for predicting pKa values for organic acids and bases is "pKalc", manufactured by CompuDrug Chemistry, Ltd. Furst Sandor utca 5 H-1136 Budapest The Marketing Director for CompuDrug Chemistry, Ltd. is Dr. Zoltan Bencz; his e-mail address is: bz@cdk-cgx.hu CompuDrug's FAX number is (0036 1) 132'25'74 CompuDrug has a marketing office in the United States. For details, please con- tact CompuDrug directly. Sincerely, S. Shapiro Abt. orale Mikrobiol. allg. Immunol. Zahnaerztl. Inst. der Univ. ZH Plattenstr. 11 Postfach CH-8028 Zuerich Internet: toukie@zui.unizh.ch We recently published a paper on the prediction of Pka's for organic oxyacids: Jour. Comp. Chem. 14, 1460 (1993). P.C. Jurs, Penn State University There is a QSAR-type program for predicting pKa's of organic acids, built on a database of some 2000 compounds. It is available through Discovery Software Inc. For pricing information, please contact Dr. Mario Dimayuga (Email address: mld8@po.cwru.edu). Dan Fercu Department of Chemistry Case Western Reserve University 10900 Euclid Ave. Cleveland, OH 44106 TO: Bill Welsh RE: Pka query on CCL See Perrin, Dempsey, and Sergeant: "pKa Prediction for Organic Acids and Bases," Chapman and Hall, London, 1981. Check with Gerald Niemi at the Univ Minn-Duluth at 218-720-4270 about computerization. Best regards from "inside the beltway" Bob +-----------------------------EPA---------------------------+ | US Environmental Protection Agency | | Office of Pollution Prevention and Toxics (Mailstop 7403) | | 401 M Street, SW, Washington, DC 20460 USA | | TEL: 202-260-1274; FAX: 202-260-1236 or 202-260-1283 | | EMAIL: lipnick.robert@epamail.epa.gov | | Robert L. Lipnick, Ph.D., Senior Chemist (QSAR-Toxicology)| +----------------------------EPA----------------------------+