From chemistry-request@server.ccl.net Sun Mar 4 07:14:22 2001 Received: from web4004.mail.yahoo.com (web4004.mail.yahoo.com [216.115.104.38]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f24CELw01842 for ; Sun, 4 Mar 2001 07:14:22 -0500 Message-ID: <20010304121421.24419.qmail@web4004.mail.yahoo.com> Received: from [151.25.243.182] by web4004.mail.yahoo.com; Sun, 04 Mar 2001 13:14:21 CET Date: Sun, 4 Mar 2001 13:14:21 +0100 (CET) From: =?iso-8859-1?q?Piero=20Ugliengo?= Reply-To: ugliengo@ch.unito.it Subject: G98 on OSF memory fault allocation To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear netters, I have succefully installed G98 rev A.7 on an a Digital OSF1 workstation equipped with 512MB memory and 1.5Gb swap area. However, as soon as I try to run a job asking for more than 100MB it immediately fails with the message: malloc failed.: Not enough space sh: 1144 Memory fault Here is the offending test job: %mem=128MB #p test opt b3lyp/aug-cc-pvdz scf=direct test hf 0 1 f h 1 hf hf 0.9241 In the following I enclose some basic info about OS release and f77 version: csh>uname -a OSF1 V4.0 878 alpha csh>f77 -what DIGITAL Fortran 77 Driver V5.0-7 DIGITAL Fortran 77 V5.0-138-3678F csh>limit cputime unlimited filesize unlimited datasize 131072 kbytes stacksize 2048 kbytes coredumpsize 0 kbytes memoryuse 506088 kbytes descriptors 4096 files addressspace 1048576 kbytes Also attached are the basic options of the g98.make file: # BSDDIR = bsd MAKELOC = -f $(BSDDIR)/g98.make BSDDIR1 = ../bsd MAKELOC1 = -f $(BSDDIR1)/g98.make UTILDIR = .. # # The utility library: # GAULIBA = util.a GAULIB = util.so # # Directory pointers only used for linking the profiling version: # GSDIR = . GDIR = ../g98 # # Standard dimensioning definitions. # # PCMDIM = -DDEFMXTS=1500 -DDEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 INCDIR = -I$(g98root)/g98 DIMENS = $(INCDIR) -DDEFMAXSHL=20000 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFMAXINFO=200 -DDEFNVDIM=257 \ -DDEFARCREC=1024 -DDEFLMAX=13 -DDEFCACHE=256 -DDEFN3MIN=10 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 \ -DDEFMAXIOP=100 -DDEFMAXCHR=1024 -DDEFMAXHEV=2000 -DDEFMAXLECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 $(PCMDIM) # # These commands are converted to "on machine command" for remote- # control compilation. # RUNCC = cc RUNAR = ar RUNRAN = ranlib RUNCPP = gau-cpp RUNFSP = gau-fsplit #RUNCPP = /lib/cpp -P -C # # Standard compilation flags: # MERGELOOPS = -DMERGE_LOOPS #AIO = -DASYNCH_IO #AIOLIB = -laio #PARFLAG = -DGAUSS_PAR PMMFLAG = -DUSE_PMM PARFLAG = -DGAUSS_PAR -DGAUSS_THPAR THLIB = -threads ALPHADEF = -DALPHA_OSF1 -DI64 -DUSE_SYSV $(DIMENS) \ $(AIO) $(MERGELOOPS) $(PARFLAG) $(PMMFLAG) -DLITTLE_END $(DEBUGP) # # OPTFLAG = -O5 COPTFLAG = -O -tune host EXTOBJ = RUNF77 = f77 #SHARE = -non_shared #FAST = -math_library fast ALPHA = -i8 -r8 -align dcommons -tune host $(FAST) $(SHARE) -trapuv $(THLIB) \ -assume noaccuracy_sensitive FFLAGS = $(OPTFLAG) $(ALPHA) CFLAGS = $(ALPHADEF) $(COPTFLAG) -trapuv NOOPT= -O0 $(ALPHA) OPT1 = -O1 $(ALPHA) OPT4 = -O4 $(ALPHA) ESSLLOC = -ldxml ESSLLIB = $(ESSLLOC) $(AIOLIB) # # Default suffixes: # Thank you for the help. Piero Ugliengo Dip. Chimica IFM Via P. Giuria 7 I-10125 Torino e-mail: piero.ugliengo@unito.it ===== Prof. Piero Ugliengo Dip. Chimica IFM Via P. Giuria, 7 I-10125 Torino ITALY Voice: +39-011-6707140 Fax: +39-011-6707855 ______________________________________________________________________ Do You Yahoo!? Il tuo indirizzo gratis e per sempre @yahoo.it su http://mail.yahoo.it From chemistry-request@server.ccl.net Sun Mar 4 08:12:09 2001 Received: from smtp2.nikoma.de ([212.122.128.25]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f24DC9w02095 for ; Sun, 4 Mar 2001 08:12:09 -0500 Received: from cosmologic.de (dialin95.pg4-nt.dusseldorf.nikoma.de [213.54.99.95]) by smtp2.nikoma.de (8.9.3/8.9.3) with ESMTP id OAA56035; Sun, 4 Mar 2001 14:11:48 +0100 (CET) (envelope-from andreas.klamt@cosmologic.de) Message-ID: <3AA20840.D259D096@cosmologic.de> Date: Sun, 04 Mar 2001 10:17:52 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Jeremy Greenwood CC: chemistry@ccl.net Subject: Re: CCL:Interpreting the quadrapole for aromatics References: <20010303160502.A157782@compchem.dfh.dk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jeremy, the only coordinate system which allows for a unique definition of quadrupoles for charged species is the center of charge. The center of mass has nothing to do with electric multipoles at all. But I doubt whether the quadrupole moment is the right quantity to look at, if you are interested in the aromatic ring. It is heavily influenced by the size, shape, and charge distribution of the substituents. The quadrupole moment (like any multipole moment) tells you about the long distance behaviour of the electrostatic potential, but not about the local information on the ring, which you are interested in. I suggest to look at the polarization charges as obtained in a continuum solvation method. Polarization charges t eps=infinity (in a conductor) are a very good local measure of polarity. You can take the total polarization charge on each atom of the aromatic ring as a rather good local measure of the induced pi-charge. Obviously this depends slightly on the choice of radii, but it will definitely be less biased than most of the partial charge schemes. An in addition you can visualize the polarization charges on the surface (see news under www.cosmologic.de). Presently the programs MOPAC2000, DMol3, and Turbomole print out the necessary information in COSMO calculations in a cosmo-file. Soon that should be possible with Gaussian and with GAMESS-US. Best regards Andreas Jeremy Greenwood schrieb: > > Dear all, > > I'm studying series of closely-related planar > (halogen,oxo,methyl)-substituted azines. I'm interested in how I can > interpret the multipoles, particularly the quadrapole. > Unfortunately, they are anions. > > 1) Is the quadrapole as confounded as the dipole as regards choice > of origin for an ion? The mass difference between F and Br will > disturb the centre-of-mass origin of otherwise identical anions. > > 2) Using MP2/6-311+G(3df,2p) set I get quadrapoles like > > XX = -97 YY = -83 ZZ = -66 > XY = -5.1 XZ = 0 YZ = 0 > > (orientation X, Y, 0) > > Can comparisons of e.g. ZZ and XY across the series give me an idea > about the degree of pi-density/aromaticity, and an idea about electron > density in within the ring vs. on the electronegative substituents? > > 3) Given the size, my options are HF, DFT or MP2, with large basis > set including diffuse functions. Any reason to choose one over the > other when comparing multipoles, electron density and aromaticity? > I seem to recall B3LYP has a reputation for over-estimating aromaticity. > > 4) EPS-derived atomic charges from Gaussian (e.g. MKS) seem hard to interpret > because fitting to the (origin dependent) dipole swamps the effects I am > looking at. Would multipole fitting be a good way to go, or should > I be looking at AIM or even Mullikan charges instead, bearing in > mind that these are aromatics. > > Thanks for any enlightenment, > > Jeremy > ---------------------------------------------------------------------- > Jeremy Greenwood jeremy.greenwood@i.am > Department of Medicinal Chemistry bh +45 35306117 > Royal Danish School of Pharmacy fx +45 35306040 > Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 > ---------------------------------------------------------------------- > Never underestimate the bandwidth of a truck full of 1/4 inch tapes > ---------------------------------------------------------------------- > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Sun Mar 4 01:01:44 2001 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2461hw24980 for ; Sun, 4 Mar 2001 01:01:43 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id VAA15117 for ; Sat, 3 Mar 2001 21:59:38 -0800 (PST) Received: from dial4.msi.com(146.202.9.104) by mailhost.msi.com via smap (V2.0) id xma015113; Sat, 3 Mar 01 21:59:04 -0800 Message-Id: <5.0.2.1.0.20010303212506.025306b8@sparky2.msi.com> X-Sender: jnauss@sparky2.msi.com X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Sat, 03 Mar 2001 21:26:20 -0800 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Customer Training Workshops in Mt. View, California Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a pair of 2-day workshops at the SGI Mountain View facility in Mt. View, California. On April 24-25, the workshop "Introduction to Life Science Modeling with InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling for proteins and other large biological molecules and complexes. Then on April 26-27, the "Introduction to Cerius2 for Life Sciences Workshop" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modeling experience is not assumed making this course a great place to learn molecular modeling with Cerius2. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second course. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss MSI Customer Training Programs -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Sun Mar 4 01:01:44 2001 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2461iw24981 for ; Sun, 4 Mar 2001 01:01:44 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id VAA15120 for ; Sat, 3 Mar 2001 21:59:39 -0800 (PST) Received: from dial4.msi.com(146.202.9.104) by mailhost.msi.com via smap (V2.0) id xmaa15113; Sat, 3 Mar 01 21:59:09 -0800 Message-Id: <5.0.2.1.0.20010303212622.0252a518@sparky2.msi.com> X-Sender: jnauss@sparky2.msi.com X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Sat, 03 Mar 2001 21:29:06 -0800 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Customer Training Workshops in Israel Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a pair of 2-day workshops at the Tel Aviv University in Tel Aviv, Israel. On 30 April to 1 May, the "Introduction to Cerius2 for Life Sciences Workshop" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modeling experience is not assumed making this course a great place to learn molecular modeling with Cerius2. On 2-3 May, the "Introduction to Catalyst Workshop" will be presented. This workshop is intended to introduce customers to pharmacophore generation and to the Catalyst user interface. No prior experience with molecular modeling is needed. The workshop begins with the basics of the Catalyst interface and builds to simple pharmacophore generation, selection of training sets, and three-dimensional database searching. Attendees should possess knowledge of basic UNIX commands and have a basic understanding of QSAR theory. Fees for each 2-day course are US$1000 commercial, US$500 government, and US$400 academic. However, register for both courses and receive a 25% discount for the second course. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss MSI Customer Training Programs -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752