From chemistry-request@server.ccl.net Tue Mar 13 05:17:34 2001 Received: from mail1.rrz.Uni-Koeln.DE (mail1.rrz.Uni-Koeln.DE [134.95.100.208]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DAHXw14922 for ; Tue, 13 Mar 2001 05:17:34 -0500 Received: from campfire.rrz.Uni-Koeln.DE (IDENT:39358@campfire.rrz.Uni-Koeln.DE [134.95.19.27]) by mail1.rrz.Uni-Koeln.DE (8.9.3/8.9.3) with ESMTP id LAA27137 for ; Tue, 13 Mar 2001 11:17:33 +0100 (MET) Received: (from a0580@localhost) by campfire.rrz.Uni-Koeln.DE (8.9.1a/8.9.1) id LAA03361 for chemistry@ccl.net; Tue, 13 Mar 2001 11:17:29 +0100 (MET) Date: Tue, 13 Mar 2001 11:17:29 +0100 From: Lars Packschies To: chemistry@ccl.net Subject: Re: CCL:Redhat/G98/PGI - Error Message-ID: <20010313111728.B19643@campfire.rrz.Uni-Koeln.DE> References: <20010312111419.E19987@campfire.rrz.Uni-Koeln.DE> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="OXfL5xGRrasGEqWY" Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20010312111419.E19987@campfire.rrz.Uni-Koeln.DE>; from packschies@rrz.uni-koeln.de on Mon, Mar 12, 2001 at 11:14:20AM +0100 --OXfL5xGRrasGEqWY Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hi All, thank you all for quick and helpful answers. The "easiest" way to get rid of the compiler stops was to change each of the two lines $(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0402.o \ $(EXTRAS) $(GAULIB) $(LIBS) and $(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0609.o \ $(EXTRAS) $(GAULIB) $(LIBS) into $(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a $(EXTRAS) \ $(GAULIB) $(LIBS) (Interestingly, I did not have to change the part containing link 806) A friend mailed an i386.make which seemed to originate from gaussian inc., which differs mainly in the blocks concerning links 302/307/324/701/703/1101/1110, 402, 609 and 806 - which are just "commented out". If anybody wants to have a look at it, I'd be happy to know if it's really a "gaussian inc." version. Just drop an Email. Gaussian compiles with both variants. At the moment, I'm testing. Another question arose from testing - Maybe I post it in this list under another Subject. Enclosed you find part of a UNIX "diff"-result with two output files from test001.com. One was computed on a SUN sparcII-Version of g98.A7, the other one on this Linux PIII machine. Why do these molecular orbital coefficients differ ? (attachment: Lines with < in the beginning are from the sparc machine, > from the i386(PIII)) The computed energies seem to be ok... Sorry if this is a dumb question. example: (sparc) Molecular Orbital Coefficients (REAL PART) 1 2 3 4 5 (SGU)--O (SGG)--O (SGG)--O (SGU)--O (SGU)--O EIGENVALUES -- -20.42283 -20.42220 -1.54274 -0.99559 -0.66338 1 1 O 1S 0.70297 0.70367 -0.16926 0.18557 0.00000 (i386) Molecular Orbital Coefficients (REAL PART) 1 2 3 4 5 (SGU)--O (SGG)--O (SGG)--O (SGU)--O (SGU)--O EIGENVALUES -- -20.42283 -20.42220 -1.54274 -0.99559 -0.66338 1 1 O 1S 0.70297 -0.70367 0.16926 0.18557 0.00000 Thanks to all who helped ! Cheers, Lars -- ,H + Dr. Lars Packschies ZAIK/RRZK, Robert-Koch-Str.10 + H H O | Chemistry Dpt. Support D-50931 Cologne | `O-H. | ,' `H | Comp.Dpt., Univ. of Cologne Phn (+49)221-478-7022 | `O-H + Packschies@rrz.uni-koeln.de Fax (+49)221-478-5568 + --OXfL5xGRrasGEqWY Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="test001.log.diff" 1c1 < Entering Gaussian System, Link 0=/Vol/chemie/libexec/g98.A7/g98/g98 --- > Entering Gaussian System, Link 0=/vol/chemie/libexec/g98.A7_s/g98/g98 3,4c3,7 < /Vol/chemie/libexec/g98.A7/g98/l1.exe /scratch/a0580/scratch/Gau-10172.inp -scrdir=/scratch/a0580/scratch/ < Entering Link 1 = /Vol/chemie/libexec/g98.A7/g98/l1.exe PID= 10173. --- > /vol/chemie/libexec/g98.A7_s/g98/l1.exe /scratch/a0580/scratch/Gau-9441.inp -scrdir=/scratch/a0580/scratch/ > Default is to use a total of 4 processors: > 4 via shared-memory > 1 via Linda > Entering Link 1 = /vol/chemie/libexec/g98.A7_s/g98/l1.exe PID= 9457. 84,87c87,91 < ********************************************* < Gaussian 98: x86-Linux-G98RevA.7 11-Apr-1999 < 12-Mar-2001 < ********************************************* --- > ************************************************* > Gaussian 98: Sun-SVR4-Unix-G98RevA.7 11-Apr-1999 > 12-Mar-2001 > ************************************************* > Default route: SCF=DIRECT 98,99c102,103 < Leave Link 1 at Mon Mar 12 15:26:31 2001, MaxMem= 0 cpu: 0.2 < (Enter /Vol/chemie/libexec/g98.A7/g98/l101.exe) --- > Leave Link 1 at Mon Mar 12 15:30:19 2001, MaxMem= 0 cpu: 0.2 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l101.exe) 109,110c113,114 < Leave Link 101 at Mon Mar 12 15:26:31 2001, MaxMem= 6291456 cpu: 0.1 < (Enter /Vol/chemie/libexec/g98.A7/g98/l202.exe) --- > Leave Link 101 at Mon Mar 12 15:30:20 2001, MaxMem= 8257536 cpu: 0.2 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l202.exe) 142,143c146,147 < Leave Link 202 at Mon Mar 12 15:26:32 2001, MaxMem= 6291456 cpu: 0.1 < (Enter /Vol/chemie/libexec/g98.A7/g98/l301.exe) --- > Leave Link 202 at Mon Mar 12 15:30:21 2001, MaxMem= 8257536 cpu: 0.3 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l301.exe) 160,161c164,165 < Leave Link 301 at Mon Mar 12 15:26:32 2001, MaxMem= 6291456 cpu: 0.1 < (Enter /Vol/chemie/libexec/g98.A7/g98/l302.exe) --- > Leave Link 301 at Mon Mar 12 15:30:22 2001, MaxMem= 8257536 cpu: 0.2 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l302.exe) 165,166c169,170 < Leave Link 302 at Mon Mar 12 15:26:33 2001, MaxMem= 6291456 cpu: 0.8 < (Enter /Vol/chemie/libexec/g98.A7/g98/l303.exe) --- > Leave Link 302 at Mon Mar 12 15:30:26 2001, MaxMem= 8257536 cpu: 2.3 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l303.exe) 168,169c172,173 < Leave Link 303 at Mon Mar 12 15:26:34 2001, MaxMem= 6291456 cpu: 0.2 < (Enter /Vol/chemie/libexec/g98.A7/g98/l311.exe) --- > Leave Link 303 at Mon Mar 12 15:30:28 2001, MaxMem= 8257536 cpu: 1.1 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l311.exe) 174,175c178,179 < Leave Link 311 at Mon Mar 12 15:26:34 2001, MaxMem= 6291456 cpu: 0.0 < (Enter /Vol/chemie/libexec/g98.A7/g98/l314.exe) --- > Leave Link 311 at Mon Mar 12 15:30:29 2001, MaxMem= 8257536 cpu: 0.1 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l314.exe) 182,183c186,187 < Leave Link 314 at Mon Mar 12 15:26:34 2001, MaxMem= 6291456 cpu: 0.0 < (Enter /Vol/chemie/libexec/g98.A7/g98/l401.exe) --- > Leave Link 314 at Mon Mar 12 15:30:30 2001, MaxMem= 8257536 cpu: 0.1 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l401.exe) 188,190c192,194 < Leave Link 401 at Mon Mar 12 15:26:35 2001, MaxMem= 6291456 cpu: 0.6 < (Enter /Vol/chemie/libexec/g98.A7/g98/l503.exe) < TCache will use 6028910 words for buffer space. --- > Leave Link 401 at Mon Mar 12 15:30:33 2001, MaxMem= 8257536 cpu: 1.5 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l503.exe) > TCache will use 7994990 words for buffer space. 208c212 < 5 -0.175338629012157D+03 --- > 5 -0.175338629012158D+03 219c223 < TCache kept 21 files containing 1192 words out of a limit of 6028910 --- > TCache kept 21 files containing 1192 words out of a limit of 7994990 221,222c225,226 < Leave Link 503 at Mon Mar 12 15:26:35 2001, MaxMem= 6291456 cpu: 0.1 < (Enter /Vol/chemie/libexec/g98.A7/g98/l601.exe) --- > Leave Link 503 at Mon Mar 12 15:30:33 2001, MaxMem= 8257536 cpu: 0.0 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l601.exe) 242,251c246,255 < 1 1 O 1S 0.70297 -0.70367 0.16926 0.18557 0.00000 < 2 2S 0.01949 -0.01273 -0.57792 -0.77599 0.00000 < 3 2PX 0.00000 0.00000 0.00000 0.00000 0.40517 < 4 2PY 0.00000 0.00000 0.00000 0.00000 0.23164 < 5 2PZ -0.00549 0.00006 0.16830 -0.15497 0.00000 < 6 2 O 1S -0.70297 -0.70367 0.16926 -0.18557 0.00000 < 7 2S -0.01949 -0.01273 -0.57792 0.77599 0.00000 < 8 2PX 0.00000 0.00000 0.00000 0.00000 0.40517 < 9 2PY 0.00000 0.00000 0.00000 0.00000 0.23164 < 10 2PZ -0.00549 -0.00006 -0.16830 -0.15497 0.00000 --- > 1 1 O 1S 0.70297 0.70367 -0.16926 0.18557 0.00000 > 2 2S 0.01949 0.01273 0.57792 -0.77599 0.00000 > 3 2PX 0.00000 0.00000 0.00000 0.00000 0.20765 > 4 2PY 0.00000 0.00000 0.00000 0.00000 0.41797 > 5 2PZ -0.00549 -0.00006 -0.16830 -0.15497 0.00000 > 6 2 O 1S -0.70297 0.70367 -0.16926 -0.18557 0.00000 > 7 2S -0.01949 0.01273 0.57792 0.77599 0.00000 > 8 2PX 0.00000 0.00000 0.00000 0.00000 0.20765 > 9 2PY 0.00000 0.00000 0.00000 0.00000 0.41797 > 10 2PZ -0.00549 0.00006 0.16830 -0.15497 0.00000 257,258c261,262 < 3 2PX 0.00000 0.44809 0.44914 0.36064 0.00000 < 4 2PY 0.00000 0.13050 0.30268 -0.40408 0.00000 --- > 3 2PX 0.00000 -0.42138 0.00374 0.52118 0.00000 > 4 2PY 0.00000 -0.20065 0.54160 0.14736 0.00000 262,263c266,267 < 8 2PX 0.00000 0.44809 -0.44914 -0.36064 0.00000 < 9 2PY 0.00000 0.13050 -0.30268 0.40408 0.00000 --- > 8 2PX 0.00000 -0.42138 -0.00374 -0.52118 0.00000 > 9 2PY 0.00000 -0.20065 -0.54160 -0.14736 0.00000 271,272c275,276 < 3 2PX 0.00000 0.00000 0.00000 0.00000 -0.23164 < 4 2PY 0.00000 0.00000 0.00000 0.00000 0.40517 --- > 3 2PX 0.00000 0.00000 0.00000 0.00000 -0.41797 > 4 2PY 0.00000 0.00000 0.00000 0.00000 0.20765 276,277c280,281 < 8 2PX 0.00000 0.00000 0.00000 0.00000 -0.23164 < 9 2PY 0.00000 0.00000 0.00000 0.00000 0.40517 --- > 8 2PX 0.00000 0.00000 0.00000 0.00000 -0.41797 > 9 2PY 0.00000 0.00000 0.00000 0.00000 0.20765 284,285c288,289 < 3 2PX 0.00000 0.13050 -0.30268 -0.40408 0.00000 < 4 2PY 0.00000 -0.44809 0.44914 -0.36064 0.00000 --- > 3 2PX 0.00000 -0.20065 -0.54160 0.14736 0.00000 > 4 2PY 0.00000 0.42138 0.00374 -0.52118 0.00000 289,290c293,294 < 8 2PX 0.00000 0.13050 0.30268 0.40408 0.00000 < 9 2PY 0.00000 -0.44809 -0.44914 0.36064 0.00000 --- > 8 2PX 0.00000 -0.20065 0.54160 -0.14736 0.00000 > 9 2PY 0.00000 0.42138 -0.00374 0.52118 0.00000 389c393 < Symmetry AG KE= 6.743437736562D+01 --- > Symmetry AG KE= 6.743437736563D+01 397,398c401,402 < Leave Link 601 at Mon Mar 12 15:26:36 2001, MaxMem= 6291456 cpu: 0.2 < (Enter /Vol/chemie/libexec/g98.A7/g98/l9999.exe) --- > Leave Link 601 at Mon Mar 12 15:30:36 2001, MaxMem= 8257536 cpu: 1.1 > (Enter /vol/chemie/libexec/g98.A7_s/g98/l9999.exe) 401c405 < 1\1\GINC-HOGWARTS\SP\RHF\STO-3G\O2\A0580\12-Mar-2001\0\\#P TEST STO-3G --- > 1\1\GINC-CAMPFIRE\SP\RHF\STO-3G\O2\A0580\12-Mar-2001\0\\#P TEST STO-3G 403,404c407,409 < STO-3G//STO-3G DIOXYGEN\\0,1\O\O,1,1.22\\Version=x86-Linux-G98RevA.7\ < HF=-147.578511\RMSD=6.484e-09\Dipole=0.,0.,0.\PG=D*H [C*(O1.O1)]\\@ --- > STO-3G//STO-3G DIOXYGEN\\0,1\O\O,1,1.22\\Version=Sun-SVR4-Unix-G98Rev > A.7\HF=-147.578511\RMSD=6.484e-09\Dipole=0.,0.,0.\PG=D*H [C*(O1.O1)]\\ > @ 407,410c412,415 < ERROR IS A HARDY PLANT... IT FLOURISHETH IN EVERY SOIL. < MARTIN FARQUHAR TUPPER < Job cpu time: 0 days 0 hours 0 minutes 4.3 seconds. < File lengths (MBytes): RWF= 10 Int= 1 D2E= 0 Chk= 5 Scr= 1 --- > Everywhere is walking distance if you have the time. > -- Steven Wright > Job cpu time: 0 days 0 hours 0 minutes 9.7 seconds. > File lengths (MBytes): RWF= 10 Int= 2 D2E= 0 Chk= 5 Scr= 1 412,413c417,420 < 2.38user 2.25system 0:07.97elapsed 58%CPU (0avgtext+0avgdata 0maxresident)k < 0inputs+0outputs (31801major+70723minor)pagefaults 0swaps --- > > real 19.9 > user 5.7 > sys 7.0 --OXfL5xGRrasGEqWY-- From chemistry-request@server.ccl.net Tue Mar 13 05:44:10 2001 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DAi8w15052 for ; Tue, 13 Mar 2001 05:44:08 -0500 Received: from localhost (kiran@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id LAA10566 for ; Tue, 13 Mar 2001 11:46:52 +0100 Date: Tue, 13 Mar 2001 11:46:52 +0100 (NFT) From: Kiran Boggavarapu To: chemistry@ccl.net Subject: Gaussian convergence problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am running G2 calcuclation on (CH3)2S with G98, with the default settings. I encoutered a convergence problem at MP4/6-311+G(d,p). The error message is Failed to converge in NBiSct. Error termination via Lnk1e in /usr/local/chem/g98/l502.exe. I do not know what is the problem. Can anyone suggest a solution? Thanks in advance Le Thanh Hung Department of Chemistry University of Leuven Leuven, Heverlee, Belgium From chemistry-request@server.ccl.net Mon Mar 12 23:40:01 2001 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2D4dww13479 for ; Mon, 12 Mar 2001 23:39:59 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id KAA04254 for ; Tue, 13 Mar 2001 10:07:58 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id JAA08260 for ; Tue, 13 Mar 2001 09:55:45 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Tue, 13 Mar 2001 09:55:45 +0530 (IST) From: Rajarshi Guha X-X-Sender: To: CompuChem List Subject: force fields for metals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, could anybody point me to reviews/links of force fields for metallic systems - I'm more interested in the nature of the force fields themselves rather than the applications to specific systems. TIA ------------------------------------------------------------------------- Rajarshi Guha | "If nobody makes you do it it Dept. of Chemistry | counts as fun" IIT Kharagpur. | | Hobbes email: rajarshi@presidency.com | rajarshi@cts.iitkgp.ernet.in | web : www.psynet.net/jijog | ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Mar 13 03:08:19 2001 Received: from web12211.mail.yahoo.com (web12211.mail.yahoo.com [216.136.173.145]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2D88Jw14383 for ; Tue, 13 Mar 2001 03:08:19 -0500 Message-ID: <20010313080819.30063.qmail@web12211.mail.yahoo.com> Received: from [212.50.47.114] by web12211.mail.yahoo.com; Tue, 13 Mar 2001 00:08:19 PST Date: Tue, 13 Mar 2001 00:08:19 -0800 (PST) From: "HÜLYA" KARA Subject: basis set of GD To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everyone, I have been using the GAUSSIAN-98 program. What is the most suitable basis set of Cu-Gd complex? Thank you very much for you help I am looking forward your answer. Best Wishes Hulya KARA __________________________________________________ Do You Yahoo!? Yahoo! Auctions - Buy the things you want at great prices. http://auctions.yahoo.com/ From chemistry-request@server.ccl.net Tue Mar 13 09:50:11 2001 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DEo8w16781 for ; Tue, 13 Mar 2001 09:50:09 -0500 Received: from lauca.usach.cl ([158.170.51.105]) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id f2DEkXf29445; Tue, 13 Mar 2001 10:46:33 -0400 (CST) Message-ID: <3AAE341D.697645B7@lauca.usach.cl> Date: Tue, 13 Mar 2001 10:52:13 -0400 From: Danilo Gonzalez X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, jorgevil@usc.edu, robert.latour@ces.clemson.edu Subject: Summary: Ligand binding to protein (DeltaH=0) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all! Thanks for all replies. I think that a good reference for this subject is the fellow: J. Phys. Chem. 1994, 98, 1515-1518. (sent by Abby) Thanks again to all and for the comment. Below is the question and the replies: ************************************************** I'm looking for references about systems where ligand binding to protein is carried out with Delta H = 0, that is, where the process is Entropically driven. ************************************************ Danilo, Take a look at J. Phys. Chem. 1994, 98, 1515-1518. -Abby ------------------------------- Dear Danilo, Sleigh et al. (J. Mol. Biol. (1999), 291, 393-415) have published DG, DH and TDS for a series of 20 KXK tripeptides binding to the OppA protein. All these processes are entropically driven, although DH is not zero, it is actually positive. Hope that will be of some use to you, Irilenia ---------------------------------------- Dear Danilo: The post from David Turner titled "Protease Inhibitors Entropy/Enthalpy" has a number of examples where the reaction is entropically driven (but the enthalpy was not necessarily equal to 0.00). It was posted a couple of weeks ago (2/27). The Freire articles outline some nice thermodynamic characterization of these systems. Best to you, --Ben --------------------------------------- You might find systems where the standard enthalpy change is small compared to TdeltaS but I doubt if you find a case where the quantity is zero. Consider the following process: L(aq) + P(aq) = LP(aq). One might find cases where hydrogen bonding and charge effects do not contribute to the binding of the ligand L to the protein P. However, you would always have contributions from the van der Waals interactions between L and P. Furthermore, one has to deal with the hydrophobic effect. As a result of binding, structured water around the ligand L will become more unstructured. The solvent contributes a positive entropy change to the overall process. In addition, there is an associated enthalpy change. Structured water is electronically more stable than unstructured water. Henry Frank, the father of the hydrophobic effect, observed in his later work that deltaH for the hydrophobic effect is the same order of magnitude as TdeltaS. You can't ignore the contribution of the solvent. This alone will yield a non-zero enthalpy change. However, you can select a system in which delta H is small. In other words, opt for a system where entropy changes are very very important. I suspect that any system that yields a good Hansch equation, i.e. binding correlates only with logP and not a Hammett sigma factor, will be one in which the entropy term will be very important. Corwin Hansch and Al Leo have written an excellent book on the QSAR method. It is published by the ACS. Also track down the literature for CoMFA (Comparative Molecular Field analysis). The original data set used by Tripos (steroid binding) should be one in which the TdeltaS term is much larger than the deltaH term. Wayne Steinmetz ----------------------end------------------------- From chemistry-request@server.ccl.net Tue Mar 13 13:20:55 2001 Received: from mail-a.bcc.ac.uk (mail-a.bcc.ac.uk [144.82.100.21]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DIKsw17743 for ; Tue, 13 Mar 2001 13:20:55 -0500 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-a.bcc.ac.uk with SMTP (Mailer); Tue, 13 Mar 2001 18:20:49 +0000 Reply-To: "a.oganov" From: "Artem R. Oganov" To: chemistry Subject: CCL: Summary on DFT and Mott insulators Date: Tue, 13 Mar 2001 18:19:35 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, Many thanks to those who have replied to my question (see the original question in the end of this e-mail). Here I give a summary of what the situation seems to be like with Mott insulators and their DFT description - both from the CCL replies and answers of my other colleagues. The Kohn-Sham eigenvalues and DOS don't have any strict physical meaning. The absence of the band gap in this unphysical DOS does not necessarily mean that the material is a metal; generally, band theory (even not at the LDA/GGA level) often gives zero band gaps for insulators. More rigorous approaches are based on considerations in the momentum space. These might enable the calculation of the electrical conductivity. Another possibility is the Green's function formalism. Yet, as practice shows, the Kohn-Sham orbitals resemble the more physical Hartree-Fock orbitals; they often can be rationalised using the language of chemistry. They are not completely unphysical. If we trust the Kohn-Sham orbiatls and their energies, the band gaps obtained with LDA/GGA are usually twice smaller than the experimental values; for Mott insulators LDA/GGA give zero or very small band gaps (~0.4 eV) while experiments give gaps ~4 eV. If we use B3LYP, the band gap comes out to be almost perfect, but physical properties become worse. Exchange potential is particularly important for the band gap. Spurious self-interaction, raising the energy of the occupied levels, is partly responsible for the band gap being reduced. GGA describes the properties rather well, but fails to give a band gap for FeO and gives very small gaps for other transition metal oxides. So far, GGA and B3LYP, though not perfect, are the best methods for Mott insulators. Quantum Monte Carlo has a good potential of describing such systems. Below is the only reply I have got and the original question: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ Hello, 1) The band gap problem for solids in DFT is closely related to the HOMO-LUMO gap problem for molecule. We had a recent discussion about the latter problem on CCL, that you could easily retrieved for the archives. For molecule, hybrid functional (combining HF exchange and pure DFT) yields much better orbital gap than pure DFT. I don't know if these functionals are implemented in the "solid state" package. 2) there is an error ! It is a large as the real band gap ! 3) I don't know, but a library search could gives you the answer... 4) HF gives band gap for the free electron case because of "self-interaction" term. I think that HF will provide to large band gap, then to low electrical conductivity etc..At least, that's a good starting point. ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++ -----Original Message----- From: Computational Chemistry List [mailto: ]On Behalf Of Artem R. Oganov Sent: 25 February 2001 10:45 PM To: CHEMISTRY Subject: CCL:Mott insulators and DFT Dear CCLers, I have the following question: It is known that DFT within the LDA and GGA gives no band gap for such transition metal oxides as FeO, CoO, NiO, which in fact are insulators (Mott insulators). Are there any ideas about how serious this error is? I suspect that there may be no real error: I understand that Kohn-Sham eigenvalues and electronic density of states are, strictly speaking, meaningless. Therefore, the absence of a band gap does not mean anything - even more it does not mean that the material is a metal. There might be other, more rigorous, ways to calculate the electrical conductivity from DFT - but I am not aware of any such work. On the other hand, GGA and LDA are known to reproduce many properties (elastic constants, equation of state, magnetic ordering, magnetic moments) of these oxides really well - at nearly the same level as they reproduce the properties, e.g., of MgO or NaCl. I would like to hear your ideas on: 1. The applicability of LDA/GGA to Mott insulators: can we use DFT at all, what we can and what we cannot calculate. 2. If there is any error at all, how serious it is. 3. How to calculate the electrical conductivity from DFT. Were such calculations done for any of the Mott insulators? 4. What is the best way of treating Mott insulators, especially at high pressures? LDA+U seems to be not too reliable at high pressures. Hartree-Fock would definitely give a band gap - but it gives it even for the free electron case! What else does exist? I will summarise the replies on request. Cheers, Artem R. Oganov ----------------------------------------------------- Artem R. Oganov Department of Geological Sciences University College London Gower Street London WC1E 6BT tel: +44 (020)-7679-3344 fax: +44 (020)-7387-1612 email: a.oganov@ucl.ac.uk http://slamdunk.geol.ucl.ac.uk/~artem --------------------------------------------------- From chemistry-request@server.ccl.net Tue Mar 13 13:44:24 2001 Received: from tomts8-srv.bellnexxia.net (tomts8.bellnexxia.net [209.226.175.52]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DIiOw17893 for ; Tue, 13 Mar 2001 13:44:24 -0500 Received: from mcmaster.ca ([64.228.140.150]) by tomts8-srv.bellnexxia.net (InterMail vM.4.01.03.16 201-229-121-116-20010115) with ESMTP id <20010313184224.XBMX20895.tomts8-srv.bellnexxia.net@mcmaster.ca> for ; Tue, 13 Mar 2001 13:42:24 -0500 Message-ID: <3AAE69B3.20908@mcmaster.ca> Date: Tue, 13 Mar 2001 13:40:51 -0500 From: Samantha Jenkins Organization: McMaster University User-Agent: Mozilla/5.0 (Windows; U; Win 9x 4.90; en-US; m18) Gecko/20010131 Netscape6/6.01 X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Basis sets for solid GaAs, GaP and ZnS X-Priority: 1 (highest) References: <3AA3CBBB.4AFB108F@mcmaster.ca> <3AA66AEB.64D6232A@mcmaster.ca> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, Does anyone have any basis sets optimised for GaAs, GaP and ZnS suitable for use in CRYSTAL98 calculations? Thanks, I will summarise answers From chemistry-request@server.ccl.net Tue Mar 13 12:28:17 2001 Received: from mail2.intermedia.net ([206.40.48.152]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DHSHw17558 for ; Tue, 13 Mar 2001 12:28:17 -0500 Received: from mentecolectiva.com (unverified [206.40.48.156]) by mail2.intermedia.net (Rockliffe SMTPRA 4.5.4) with SMTP id for ; Tue, 13 Mar 2001 09:27:19 -0800 Message-ID: <1916920013213172720263@mentecolectiva.com> X-EM-Version: 5, 0, 0, 9 X-EM-Registration: #3173510714C40C031530 From: "Familia Esguerra Neira" To: chemistry@ccl.net Subject: Short Budget Date: Tue, 13 Mar 2001 09:27:20 -0800 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Hello all, I would like to ask for your advice on buying a PC for running gaussian 98 and gamess-us jobs under Slackware Linux 7.1. My budget is U$4000 and I have been looking at Dell computers for the fastest machine I can get with this money. I am undecided on whether to buy a dual pentium III 933MHz or a single pentium IV 1.5 GHz processor both with 1Gb PC800 RDRAM; if any of you out there has any information as to which of this two options would work better, or other suggestion on how to invest my money in order to obtain the fastest performing machine I would greatly appreciate it. Thanking your advice, Mauricio Esguerra Neira Grupo de Quimica Teorica Universidad Nacional de Colombia From chemistry-request@server.ccl.net Tue Mar 13 14:49:35 2001 Received: from usintout01.net.bms.com (usintout01.bms.com [165.89.129.231]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DJnZw18396 for ; Tue, 13 Mar 2001 14:49:35 -0500 Received: from nsusmsg03.net.bms.com ([127.0.0.1]) by mochilla.bms.com (PMDF V5.2-32 #38470) with ESMTP id <0GA500D7ZJ2N6I@mochilla.bms.com> for chemistry@ccl.net; Tue, 13 Mar 2001 19:49:36 +0000 (GMT) Received: from bms.com ([140.176.4.228]) by nsusmsg03.net.bms.com (Netscape Messaging Server 4.15) with ESMTP id GA5J2N00.NZP; Tue, 13 Mar 2001 19:49:35 +0000 Date: Tue, 13 Mar 2001 14:48:51 -0500 From: Doree F Sitkoff Subject: software to compute dendrograms from distance matrices To: chemistry@ccl.net Cc: Doree F Sitkoff Message-id: <3AAE79A3.3D5D1EA6@bms.com> Organization: Bristol-Myers Squibb MIME-version: 1.0 X-Mailer: Mozilla 4.72 [en]C-BMY (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: Dear All, Does anyone know of software (PC or UNIX-based) that can take a distance matrix as input, perform clustering and display back results as a dendrogram - of high enough quality that it could be used for poster or publication purposes? I have investigated SAS/JMP however it appears that it cannot take a distance matrix as input - it must calculate the matrix within the program. MINITAB does appear to be able to do this, however I am wondering what other options we might have. Thanks, -Doree --- Doree Sitkoff, PhD Research Investigator Bristol-Myers Squibb, PRI doree.sitkoff@bms.com From chemistry-request@server.ccl.net Tue Mar 13 15:31:32 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DKVVw18704 for ; Tue, 13 Mar 2001 15:31:32 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu; Tue, 13 Mar 2001 14:31:57 -0600 Sender: yubo@ccl.net Message-ID: <3AAE843E.23AC887C@mail.chem.tamu.edu> Date: Tue, 13 Mar 2001 20:34:07 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: Familia Esguerra Neira CC: chemistry@ccl.net Subject: Re: CCL:Short Budget References: <1916920013213172720263@mentecolectiva.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I prefer a dual pentium III 933MHz with 1GB SDRAM (I don't think PC800 RDRAM is much faster than PC133 SDRAM and the bus speed of PIII/933 is 133 MHz). I list the prices of the most important components for your calculations. 2 PIII/933 $500 1GB SDRAM(4x256MB) $450 MSI 694D VIA Dual Socket 370 motherboard $140 40GB ATA100 Hard Drive (7200 rpm) < $150 others: monitor, video card, network card housing, mouse and keyboard So, you can build two dual PIII/933 w/1GB memory Linux machine as I suggest. Of course, you just need one monitor for them. You can remote-control them when you run QM jobs on them. Remember, this type of computer is very good for DFT calculation. Don't try POST-SCF calculations (ie CCSD) on them, or you will be very disappointed. I hope my suggestion gives you some help Sincerely Yubo Familia Esguerra Neira wrote: > Hello all, > > I would like to ask for your advice on buying a PC for running gaussian 98 > and gamess-us jobs under Slackware Linux 7.1. My budget is U$4000 and I > have been looking at Dell computers for the fastest machine I can get with > this money. > > I am undecided on whether to buy a dual pentium III 933MHz or a single > pentium IV 1.5 GHz processor both with 1Gb PC800 RDRAM; if any of you out > there has any information as to which of this two options would work > better, or other suggestion on how to invest my money in order to obtain > the fastest performing machine I would greatly appreciate it. > > Thanking your advice, > > Mauricio Esguerra Neira > Grupo de Quimica Teorica > Universidad Nacional de Colombia > > -= 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 -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Tue Mar 13 15:48:27 2001 Received: from sulu.mmm.com (sulu.mmm.com [192.28.4.21]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DKmEw18854 for ; Tue, 13 Mar 2001 15:48:14 -0500 Received: from us-joancrawford.mmm.com (us-joancrawford.mmm.com [169.10.8.201]) by sulu.mmm.com (8.8.7/8.8.7) with ESMTP id OAA04186; Tue, 13 Mar 2001 14:27:44 -0600 (CST) Subject: 01.08..26 Call For Papers -- SAMs Modeling Symposium at Summer ACS To: chemistry@ccl.net Message-ID: From: rbross@mmm.com Date: Tue, 13 Mar 2001 14:27:40 -0600 [ Converted to text by jkl from MS-WORD attachments ] [ Sorry for intrusion... ] Hi Folks, Attached could you please an invitation letter and Call for Papers for the symposium: Computational Modeling and Simulation of Self-Assembled Materials which Mario Blanco and I are co-organizing. The symposium will be held at the Chicago National ACS meeting this summer. Would you please consider submitting a paper in this rapidly developing and increasingly important field. The ACS on-line abstract service is now accepting abstracts for this meeting. The deadline for submitting abstracts is April 15, 2001. If there any questions or you would like more info could you please feel free to contact either Mario or myself. Could you also please kindly forward this to other folks you think might be interested. Thanks very much and with best regards, Rick (See attached file: SAMS_announc) (See attached file: SAMs_Symp_invite_lett) ======================================================================= Dear Colleague: This note is to invite you to participate in the symposium: Computational Modeling and Simulation of Self-Assembled Materials 222nd National American Chemical Society Meeting in Chicago, IL August 26-30, 2001 Sponsored by the Division of Colloid and Surface Chemistry Co-Sponsored by the Division of Computers in Chemistry and the Division of Fluorine Chemistry The symposium will be focused on the computational modeling and simulation of self-assembled materials such as self-assembled organic monolayers, multi-layer films, and polymers.Contributions are requested which cover a wide range of chemistries including hydrocarbon, fluorocarbon, silane-based, mixed chemistry and more.The modeling of materials as freestanding films and membranes as well as on substrates is of interest.Papers are requested for the symposium, which will cover a wide-range of molecular compounds, synthetic polymeric materials, biological compounds, and biopolymers.Contributions focused on self-organization involving both polymeric sidechains and/or backbones are of great interest.Papers are also requested employing a wide range of methodologies including for example atomistic molecular modeling and simulation approaches, mesoscale approaches, and more. In addition to presentations during the ACS meeting we plan to organize a group social event to allow for greater interaction of participants. We are also planning on publishing the proceedings in an ACS or other appropriate review series. Complementing the Computational Modeling and Simulation Symposium in the Colloids and Surfaces Division will be symposia on Gels and Self-Assembled Films, Advances at the Solid Liquid Interface, and Advanced Membrane Materials. Attached could you please find the formal Call for Papers. In addition could you please feel free to contact either of us for any additional information.Thank you very much. With best regards, co-organizer: co-organizer: Mario Blanco Rick Ross California Institute of Technology 3M Company mario@wag.caltech.edu rbross@mmm.com ============================================================================= SAMs Symposium Additional Possible Speakers CALL FOR PAPERS =============== Computational Modeling and Simulation of Self-Assembled Materials A Symposium to be held at the 222nd National American Chemical Society Meeting in Chicago, IL August 26-30, 2001 Sponsored by the Division of Colloid and Surface Chemistry Co-Sponsored by the Division of Computers in Chemistry and the Division of Fluorine Chemistry Co-Organizers: Mario Blanco, California Institute of Technology, BI 139-74, Pasadena, CA 91125 (mario@wag.caltech.edu) Rick Ross, 201-2E-23, 3M Company, St. Paul, MN 55144 (rbross@mmm.com) Summary This symposium will be focused on the computational modeling and simulation of self-assembled materials such as self-assembled organic monolayers, multi-layer films, and polymers. Contributions are requested which cover a wide range of chemistries including hydrocarbon, fluorocarbon, silane-based, mixed chemistry and more. The modeling of materials as freestanding films and membranes as well as on substrates is of interest. Papers are requested for the symposium, which will cover a wide-range of molecular compounds, synthetic polymeric materials, biological compounds, and biopolymers. Contributions focused onself-organization involving both polymeric sidechains and/or backbones are of great interest.Papers are also requested employing a wide range of methodologies including for example atomistic molecular modeling and simulation approaches, mesoscale approaches, and more. Abstract Deadline: Abstracts for talks and poster sessions are being accepted now.Deadline for submission of 150-word abstract is pril 30, 2001.The co-organizers will select approximately 28 for talks. Abstract Submission Procedure: Submit abstracts via the Online Abstract Submittal System (OASys) at www.acs.org/meetings. Identify this symposium under the Division of Colloid and Surface Chemistry and nput your abstract. For more information, please contact one of the co-organizers above. ======================================================================= From chemistry-request@server.ccl.net Tue Mar 13 17:14:37 2001 Received: from mail1.ceniai.inf.cu ([169.158.128.142]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2DMEYD00849 for ; Tue, 13 Mar 2001 17:14:35 -0500 Received: from uucp.ceniai.inf.cu (uucp.ceniai.inf.cu [169.158.128.157]) by mail1.ceniai.inf.cu (8.11.0/8.11.0) with ESMTP id f2DH9RP72498 for ; Tue, 13 Mar 2001 17:09:28 GMT Received: (from uucp@localhost) by uucp.ceniai.inf.cu (8.11.1/8.11.1) with UUCP id f2DMBH275468 for chemistry@ccl.net; Tue, 13 Mar 2001 17:11:17 -0500 (CST) (envelope-from peralta@ceinpet.inf.cu) Received: from ceinpet.inf.cu ([192.168.1.188]) by hermes.ceinpet.inf.cu (8.8.7/8.8.7) with ESMTP id MAA20513 for ; Tue, 13 Mar 2001 12:11:37 -0600 Message-ID: <3AAE98CD.9AFB57D1@ceinpet.inf.cu> Date: Tue, 13 Mar 2001 17:01:49 -0500 From: Alejandro =?iso-8859-1?Q?Gonz=E1lez?= Peralta Organization: CEINPET X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: Basis set for Co3+ Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all: I'm looking for basis sets for Cobalt for being used in Co3+, like in perovskites (LaCoO3). I'm using CRYSTAL98. Any suggestion will be appreciated. Thanks in advance, Alejandro ____________________ Alejandro G. Peralta Unidad de Catalisis CEINPET Ciudad Habana Cuba ____________________ From chemistry-request@server.ccl.net Tue Mar 13 20:38:13 2001 Received: from magnum.cooper.edu ([199.98.16.4]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2E1cCD01534 for ; Tue, 13 Mar 2001 20:38:12 -0500 Received: by magnum.cooper.edu id AA28747 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Tue, 13 Mar 2001 20:32:07 -0500 Date: Tue, 13 Mar 2001 20:32:07 -0500 (EST) From: "Robert Q. Topper" To: CHEMISTRY@ccl.net Cc: ECCC7 Scientific Organizing Committee -- Dave Ferguson , Francis Muguet , "J.M.L. Gershom Martin" , Mark Tuckerman , Yi-Ping Liu , ECCC7 Web Organizing Commitee -- HOPKINS BOB , Dominic Coluccio , Heather Hauck , LENT CHRISTOPHER P , MISZPUTEN RENEE , renee@hamaoui.com, renee_miszputen@att.net, Sung-Hyun Son Subject: ECCC7 Information Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ECCC7 authors and participants, As you've probably noticed, the website for ECCC7 (http://eccc7.cooper.edu) is up and running! The conference is running using Discus Pro, the commercial version of the same software used for ECCC6. Many thanks to Heather Hauck, who designed the "look and feel" of the board and the new conference graphic, as well as to the rest of the ECCC7 web team. Please visit the site at your earliest convenience and register, and encourage your coauthors and colleagues to do the same. This is necessary so that you can set up and customize your account. It will also be necessary for you to post questions and answers. Finally, we really need you to register so that we can have an accurate headcount of participants. All submitting authors are required to register. To register, go to the Utilities menu on the left-hand side of the initial screen, click on "Your Account," and click on "Instant Registration." You will receive your initial password by email. Then you can log into your account and edit your profile, adding information such as your institutional affiliation, your personal web site's URL, and even a photo of yourself (this is strongly encouraged). Feel free to experiment with the discussion format in the "Suggestion Box" topic. There are lots of fun options within Discus which you can use to enliven your comments (if you choose). You can find information on how to format posts (add italics, etc.), add pictures and clip art, and so forth by clicking on "Formatting" under the Documentation menu. Instead of HTML, Discus uses its own (simpler) formatting commands. One caveat; the Greek fonts do not seem to display properly on many UNIX-based web browsers (because they may not have the Symbol font installed). Please remember that your contribution should be completely ready by Monday, March 26. Whether you are preparing a poster or a paper, your contribution should be viewable with a conventional web browser (i.e. it should be an HTML document or site). When your presentation is completely finished, please send the URL of the entry point to me at topper@cooper.edu before March 26. If you have requested that your presentation be served directly > from our server rather than your local site, you can simply provide the URL to us when it is ready and we will upload your entire presentation onto our own site. Alternatively, you can put the entire presentation into an archive and tell us where we can pick it up by anonymous FTP. Archives of smaller presentations can simply be sent to me by email. I encourage you to take maximum advantage of the Web's capabilities for displaying and sharing scientific information. Some useful resources can be found by clicking on "Announcements" and then "Links for WWW Publication of Molecular Structures and Other Chemical Information." Please let me know if you have any questions, and welcome to ECCC7! Best regards, Robert ***************************************************************************** ELECTRONIC COMPUTATIONAL CHEMISTRY CONFERENCE APRIL 2001 http://eccc7.cooper.edu ***************************************************************************** Robert Q. Topper, Ph.D. email: topper@cooper.edu Associate Professor of Chemistry phone: (212) 353-4378 School of Engineering fax: (212) 353-4341 The Cooper Union for the Advancement of Science and Art subway: take the 6 to Astor Place 51 Astor Place or the N/R to 8th street New York, NY 10003 and you're there! ***************************************************************************** http://www.cooper.edu/engineering/chemechem/ *****************************************************************************