From smori@chem.s.u-tokyo.ac.jp Thu Dec 5 04:51:16 1996 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by www.ccl.net (8.8.3/950822.1) id EAA19903; Thu, 5 Dec 1996 04:37:19 -0500 (EST) Received: from [133.11.6.112] (smori.chem.s.u-tokyo.ac.jp [133.11.6.112]) by utsc.s.u-tokyo.ac.jp (8.7.6+2.6Wbeta7/3.4W2) with SMTP id SAA27690 for ; Thu, 5 Dec 1996 18:36:53 +0900 (JST) Message-Id: <199612050936.SAA27690@utsc.s.u-tokyo.ac.jp> X-Sender: smori@utsc3.chem.s.u-tokyo.ac.jp X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Thu, 5 Dec 1996 18:37:58 +0900 To: chemistry@www.ccl.net From: smori@chem.s.u-tokyo.ac.jp (Seiji Mori) Subject: CCL:dynamic(al) correlation-summary2 In two weeks ago, I posted the summary about a terminology of "dynamic(al) correlation". In this time, all replies are not the same, one said "dynamical" and "dynamic " in correlation are the same. the other said that dynamical correlation is prefered or must be used. Later, in Nov.22, Professor E. Lewars, Trent University, corresponded again that dynamical was old-fashioned thus dynamic was prefered. Recently, I also asked the same question to Professor N. C. Handy, Cambridge, in his stay in Tokyo, and he told me that "dynamical" and "dynamic" are the same meaning. I must remind these novel answers. In sum, "dynamical" is major used in papers but "dynamic" is also acceptable. I also see the latter term in journals. Thank you for all responders. Sincerely yours, Seiji Mori #################################################### Seiji Mori.(M.Sc.) Graduate student Lab. of Physical Organic Chemistry Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN. email:smori@utsc.s.u-tokyo.ac.jp smori@utsc3.chem.s.u-tokyo.ac.jp --- http://www.chem.s.u-tokyo.ac.jp/Students/smori.html #################################################### From d.w.price@reading.ac.uk Thu Dec 5 08:51:18 1996 Received: from sussdirt.rdg.ac.uk for d.w.price@reading.ac.uk by www.ccl.net (8.8.3/950822.1) id IAA21188; Thu, 5 Dec 1996 08:32:29 -0500 (EST) Received: from indyp (actually host scsgind2) by sussdirt.rdg.ac.uk; Thu, 5 Dec 1996 13:32:07 +0000 Received: from Indyp by indyp via SMTP (940816.SGI.8.6.9/930416.SGI) for id NAA00459; Thu, 5 Dec 1996 13:31:59 GMT Sender: dave@reading.ac.uk Message-ID: <32A6CECF.446B@reading.ac.uk> Date: Thu, 05 Dec 1996 13:31:59 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) To: Comp Chem Mailing List Subject: Ab initio treatment of metals MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Does anyone have any suggestions and references as to the best ab initio method for metals? Please let me know as my cluster calculations are not working as well as I had hoped. Cheers, Dave ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 6AD U.K. ------------------------------------------------------------------------ From anina01@iona.cryst.bbk.ac.uk Thu Dec 5 09:51:18 1996 Received: from iona.cryst.bbk.ac.uk for anina01@iona.cryst.bbk.ac.uk by www.ccl.net (8.8.3/950822.1) id IAA21126; Thu, 5 Dec 1996 08:11:29 -0500 (EST) Received: from jura.cryst.bbk.ac.uk by iona.cryst.bbk.ac.uk; (5.65v3.2/2.1/09Sep96-1332PM) with SMTP id <9612051314.AA17674@iona.cryst.bbk.ac.uk>; Thu, 5 Dec 1996 13:14:36 GMT Received: from localhost by jura.cryst.bbk.ac.uk (931110.SGI) id AA11094; Thu, 5 Dec 96 13:14:35 GMT Date: Thu, 5 Dec 1996 13:14:35 +0000 (GMT) From: Alex Ninaber X-Sender: anina01@jura.cryst.bbk.ac.uk To: CHEMISTRY@www.ccl.net Subject: Gamess Problems Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I am trying to compile Gamess (not the UK version) for several SGI machines. My final goal is to calculate the electrostatic potential felt by a test charge at different points. My question is this: Whatever I try, I never get any results. The energy calculation seems to work fine, but the program does not generate any points. Is the program buggy, or is it me? To put it in other words: should the following script work? : (Don't mind the point group, it is a test script) $CONTRL SCFTYP=RHF EXETYP=RUN RUNTYP=ENERGY COORD=UNIQUE $END $CONTRL MOLPLT=.TRUE. ICHARG=0 $END $BASIS GBASIS=N31 NGAUSS=6 $END $GUESS GUESS=HUCKEL $END $ELPOT IEPOT=1 WHERE=PDC OUTPUT=PUNCH $END $PDC PTSEL=CONNOLLY $END $DATA Benzene C1 C1 6.0 1.072 -0.206 0.069 H1 1.0 1.147 0.865 0.192 C2 6.0 2.236 -0.978 -0.093 H2 1.0 3.205 -0.500 -0.095 C3 6.0 2.139 -2.372 -0.252 H3 1.0 3.033 -2.965 -0.377 C4 6.0 0.877 -2.994 -0.250 H4 1.0 0.802 -4.064 -0.372 C5 6.0 -0.287 -2.221 -0.088 H5 1.0 -1.256 -2.699 -0.086 C6 6.0 -0.190 -0.827 0.072 H6 1.0 -1.084 -0.234 0.196 $END Alex Ninaber anina01@iona.cryst.bbk.ac.uk From sophie@ms532u02.u-3mrs.fr Thu Dec 5 10:51:18 1996 Received: from ms532u02.u-3mrs.fr for sophie@ms532u02.u-3mrs.fr by www.ccl.net (8.8.3/950822.1) id KAA22200; Thu, 5 Dec 1996 10:49:26 -0500 (EST) From: Received: by ms532u02.u-3mrs.fr (AIX 3.2/UCB 5.64/4.03) id AA16121; Thu, 5 Dec 1996 16:50:36 +0100 Message-Id: <9612051550.AA16121@ms532u02.u-3mrs.fr> Subject: CCL:torsion angles list in Discover ? To: CHEMISTRY@www.ccl.net Date: Thu, 5 Dec 1996 16:50:36 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23alpha2] Content-Type: text Hello I am working with Discover 95.0, and I would like to know if someone has already solve the following problem. List all the possible dihedral angles for a given molecule and store them (values and atoms) in a table to be able to use it (the table :) ) later. Thanks in advance :) I will reply the corresponding BCTL script if someone help me to interested person. Philippe Camelio Lab. de Stereochimie Marseille, France From varnai@bellatrix.pcl.ox.ac.uk Thu Dec 5 11:36:33 1996 Received: from oxmail4.ox.ac.uk for varnai@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA22207; Thu, 5 Dec 1996 10:50:00 -0500 (EST) Received: from joule.pcl.ox.ac.uk by oxmail4 with SMTP (PP) with ESMTP; Thu, 5 Dec 1996 15:48:58 +0000 Received: from bellatrix (bellatrix.pcl.ox.ac.uk [163.1.21.231]) by joule.pcl.ox.ac.uk (8.6.10/8.6.5) with ESMTP id PAA06420 for <@joule.pcl:CHEMISTRY@www.ccl.net>; Thu, 5 Dec 1996 15:48:51 GMT Received: by bellatrix (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id PAA17322; Thu, 5 Dec 1996 15:50:36 GMT From: varnai@bellatrix.pcl.ox.ac.uk (Peter Varnai) Message-Id: <199612051550.PAA17322@bellatrix> Subject: MOPAC question To: CHEMISTRY@www.ccl.net Date: Thu, 5 Dec 1996 15:50:31 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Dear MOPAC Users, Can You 1, define geometry in mixed internal and cartesian coordinates? 2, follow an optimization structure by structure? 3, give me a hint what the problem with dumping to restart file is, if sue: unformatted io not allowed, apparent state: unit 9 named am1_ts2_end.res, last format: lately writing sequential unformatted external IO message comes to the shell, and the program aborts? Thank You, Peter From alper@moldyn.com Thu Dec 5 11:51:20 1996 Received: from photon.com for alper@moldyn.com by www.ccl.net (8.8.3/950822.1) id LAA22662; Thu, 5 Dec 1996 11:48:06 -0500 (EST) Received: from bart.moldyn.com ([172.16.2.14]) by gateway.photon.com with SMTP id <5901-1>; Thu, 5 Dec 1996 08:40:56 -0800 Received: by bart.moldyn.com (940816.SGI.8.6.9/940406.SGI.AUTO) id LAA23216; Thu, 5 Dec 1996 11:51:55 -0500 From: alper@moldyn.com (Howard Alper) Message-Id: <199612051651.LAA23216@bart.moldyn.com> Subject: Summary of QM/MM question To: CHEMISTRY@www.ccl.net Date: Thu, 5 Dec 1996 08:51:52 -0800 Cc: alper@bart.moldyn.com (Howard Alper) Reply-To: alper@bart.moldyn.com X-Mailer: ELM [version 2.4 PL22] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi all, On Nov. 15th I wrote the ccl, asking some questions about the use of combined Quantum/Classical forcefields (QM/MM). My original query was: ________________________________________________________________________ Hi all, I will be doing simulations using the mixed or combined quantum/classical forcefield in CHARMM. I have several questions, and would appreciate your help: 1) Does anyone know of improvements in combined-forcefield codes as regards efficiency? I am asking because I may designate a non-insigificant number of atoms as quantum atoms, and so the CPU time will go up drastically. 2) Does anyone know how the CPU time/md step changes as a function of the number of atoms designated as quantum atoms? 3) Is there any information on the relative amounts of time spent on calculating the interactions between quantum atoms, vs. the time spent on interactions between quantum and classical atoms? I will summarize the results and post to the list. Thanks. Howard ________________________________________________________________________ Now here are your responses: ________________________________________________________________________ Rick Venable: On Fri, 15 Nov 1996, Howard Alper wrote: > I will be doing simulations using the mixed or combined quantum/classical > forcefield in CHARMM. I have several questions, and would appreciate your > help: There's CHARMM, and then there's CHARMM; the answer is version dependent. There are many recent changes in this area found only in CHARMM the c25a2 version. > 1) Does anyone know of improvements in combined-forcefield codes as > regards efficiency? I am asking because I may designate a non-insigificant > number of atoms as quantum atoms, and so the CPU time will go up drastically. There's QM, and then there's QM; CHARMM c25a2 supports both AMPAC (semi-empirical) and GAMESS (ab initio) codes, but only one of these may be included in a given executable. The determination is made at compile time via preprocessor keywords (QUANTUM or GAMESS) in the pref.dat configuration file. For AMPAC (the QUANTUM keyword in pref.dat), I've found that modifying the quantum.mk Fortran compiler options from the default level 0 optimization to level 2 with static array storage leads to a 4-fold speedup for the testcase; true for c24 versions as well. CHARMM c25a2 includes a parallel version of GAMESS, so that both the MD and the QM portion can be run on various parallel architectures, from workstations linked by FDDI to high end systems like the SP2 (IBM) and T3D (Cray). I don't believe the AMPAC code runs in parallel, though. > 2) Does anyone know how the CPU time/md step changes as a function of the > number of atoms designated as quantum atoms? > > 3) Is there any information on the relative amounts of time spent on > calculating the interactions between quantum atoms, vs. the time spent > on interactions between quantum and classical atoms? The best person to answer these questions is Milan Hodoscek, who did a lot of the integration of CHARMM and GAMESS, and has been instrumental in re-designing the QM/MM interface to include such features as blurred charges (rather than point charges) and providing a common interface for both QM code sets. His E-mail address is milan@kihp6.ki.si For more general info, see the c25a2 CHARMM documentation files at http://www.mgsl.dcrt.nih.gov/Charmm/ especially the gamess.doc file. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov \/ |=| position of the FDA; for that, http://nmr1.cber.nih.gov/venable.html |=| see http://www.fda.gov ) ________________________________________________________________________ A. J. Turner: I am not aware of anything faster than Charmm - as Charmm is about the only am1 implementation that I am aware of!. At ab-initio - you can bank on all the time being in the 2 electron integrals - so the scf/mm interaction is cheep (unless you have a very small scf and thousands of mm atoms). At am1 / charmm things seem quite different. Say with 1500 mm atoms - you need about 20 heavies and 20 lights before the scf takes longer than the qm/mm interactions. The plain fastest is to use non-polarised qm/mm with an scf - but that is not anything like as 'good'. I hope that helps a little. Let me know if you want anything else on the subkect Alex ________________________________________________________________________ Milan Hodoscek: Howard> 3) What is your experience with the effect on the CPU time Howard> of using the mixed forcefield? More specifically: Howard> 3a) Do you have any knowledge of how the CPU time for a Howard> combined-forcefield dynamics simulation goes up with the # Howard> atoms designated as quantum? What other variables might Howard> affect this trend (connectivity between quantum atoms, Howard> nonbonded cutoffs, quality of quantum calculations, etc)? The main thing is number of QM atoms. It goes like N**3 Howard> 3b) If one can think of the quantum calculations as of two Howard> tpes, those between quantum atoms and those between Howard> quantum and classical atoms, what % of the total quantum Howard> forcefield calculation time is taken up with the former Howard> and latter calculations? (I am assuming that the quantum Howard> calculation can be bnroken up into intra-quantum and Howard> quantum-classical. Is this the way the calculations work? Howard> If not (in general) how do you they work to produce forces Howard> between quantum atoms and between quantum and classical Howard> atoms?) Everything is coupled together and the whole calculation is performed on each energy call, e.g. every step in the dynamics run. Milan ________________________________________________________________________ I thank everyone so much for their responses. Howard -- Dr. Howard Alper Moldyn Inc. 955 Massachusetts Avenue Fifth Floor Cambridge, MA 02139-3180 617-354-3124 x19 email: alper@moldyn.com - helping molecules find happiness for over a 10th of a century. From berriz@chasma.harvard.edu Thu Dec 5 12:51:21 1996 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.8.3/950822.1) id MAA23077; Thu, 5 Dec 1996 12:28:32 -0500 (EST) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA15354; Thu, 5 Dec 1996 12:26:58 -0500 Date: Thu, 5 Dec 1996 12:26:58 -0500 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9612051726.AA15354@chasma.harvard.edu> To: chemistry@www.ccl.net Subject: ISO software for CPU allocation over networked workstations Dear netters: At the risk of getting myself summarily booted out of here for gross inappropriateness, I would like to ask the readership a question about CPU allocation software. Presently, the "CPU allocation problem" is an endless source of conflict among lab members. Partly due to due to historical reasons and partly due to the KrazyKwilt heterogeneity of our present hardware, we have not being able to agree on a CPU allocation policy that is efficient, productive, and fair to all users. (Our jobs range >from minor interactive ones such as word processing to background multi-CPU-day simulations). We are now in the process of overhauling our lab's computer system, and the question of CPU allocation keeps rearing its ugly head. If the choice hardware configuration has any bearing on the kinds of CPU allocation policies that can be easily and effectively implemented, we want to make sure we choose the one with the least nightmarish options. One possibility we are considering for the new system is simply a cluster of reasonably powerful (e.g. Pentium Pro), at roughly one machine per lab member. To avoid wasting CPU time, however, we would like to set it up as follows: to give everyone an adequate baseline level of computational power, each individual would have top priority on his/her assigned machine (i.e. his/her jobs would be "native" in this machine), BUT any other member of the group would still be allowed to run low-priority "foreign" jobs on it as well. Each machine would be set up such that its system would allocate little or no CPU to all foreign jobs whenever at least one native job was running. This setup, however, is not yet ideal, since it leaves the problem of assigning foreign jobs to the users, which means that it would be likely that machines would go idle, or that the foreign job load over the entire cluster would become unbalanced. Our quixotic dream, therefore, is to find job management software that would periodically monitor CPU usage over all our networked workstations, and *move around* foreign jobs as necessary to avoid idle CPU's and load imbalances. Is this even technically possible? Does software to do this exist? If so, for which hardware platforms is it available? Another problem with this idea is the same problem with lab benches: the lab's size fluctuates, so times will certainly come when we have more people than machines. As with physical benches, I suppose that this will require some "doubling up"... If anyone has experience with or general comments and criticism about such a set up, I would be very grateful to hear about it. Thank you very much in advance for all your help. I'll summarize the responses (I'll try at least). Gabriel Berriz berriz@chasma.harvard.edu Department of Chemistry and Chemical Biology Harvard University From katsu@po.yb.cc.yamaguchi-u.ac.jp Thu Dec 5 20:51:24 1996 Received: from apl.yb.cc.yamaguchi-u.ac.jp for katsu@po.yb.cc.yamaguchi-u.ac.jp by www.ccl.net (8.8.3/950822.1) id UAA25960; Thu, 5 Dec 1996 20:22:00 -0500 (EST) Received: (from katsu@localhost) by apl.yb.cc.yamaguchi-u.ac.jp (8.6.12+2.4W/3.3W yamaguchi-u[96/02/01]) id KAA20837 for chemistry@www.ccl.net; Fri, 6 Dec 1996 10:21:21 +0900 Date: Fri, 6 Dec 1996 10:21:21 +0900 From: tsuyoshi-katsuragi Message-Id: <199612060121.KAA20837@apl.yb.cc.yamaguchi-u.ac.jp> To: chemistry@www.ccl.net Subject: summary:docking software Dear netters; A few months ago, I posted the request described bellow. > > I am looking for a software to dock a guest molecule into >a host molecule. > If anyone know the information about the sofware, Please >tell me that. > I have received some good reply to my question. Thanks for all who have helped. There are two useful software 'AutoDock' and 'Dock' I send you the two replies about these software. ---------------------------------------------------------------- > >From Christoph.Sotriffer@uibk.ac.at Mon Nov 11 20:39:30 1996 > > >Have a look at > > http://www.scripps.edu/pub/olson-web/doc/autodock/ > >to see whether the AutoDock program is the right thing for you. > ---------------------------------------------------------------------------------- > >From hendrix@polonius.ucsf.EDU Tue Nov 12 03:58:12 1996 > >Please look at the UCSF DOCK web page. We might have what you are >looking for. The URL is >www.cmpharm.ucsf.edu/kuntz/dock.html > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >Donna K. Hendrix >Kuntz Laboratory, UCSF Phone: (415) 476-3312 >513 Parnassus Avenue, Box 0446 FAX: (415) 476-9124 >San Francisco, CA 94143-0446 e-mail: hendrix@cgl.ucsf.edu >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ----------------------------------------------------------------------------- Sincerely Yours Tsuyoshi Katsuragi Tsuyoshi Katsuragi /////////////////////////////// ------------------ Laboratory of Biological Chemistry, Department of Biological Science, Faculty of Agriculture, Yamaguchi University 1677-1, Yoshida, Yamaguchi, 753, Japan E-mail: katsu@po.yb.cc.yamaguchi-u.ac.jp Tel. 81-0839-33-5855 (co/Prof ide) //////////////////////////////////////////////////