From blonski@alumina.rutgers.edu Tue Nov 23 00:49:51 1993 Received: from alumina.rutgers.edu for blonski@alumina.rutgers.edu by www.ccl.net (8.6.4/930601.1506) id XAA06102; Mon, 22 Nov 1993 23:54:30 -0500 Received: by alumina.rutgers.edu (5.59/SMI4.0/RU1.5/3.08) id AA02208; Mon, 22 Nov 93 23:54:16 EST From: blonski@alumina.rutgers.edu (Slawomir Blonski) Message-Id: <9311230454.AA02208@alumina.rutgers.edu> Subject: Re: Excimer Calculations To: rovshan@atlas.chemistry.uakron.edu (Rovshan G. Sadygov) Date: Mon, 22 Nov 1993 23:54:15 -0500 (EST) Cc: chemistry@ccl.net In-Reply-To: <9311222326.AA05325@atlas.chemistry.uakron.edu> from "Rovshan G. Sadygov" at Nov 22, 93 06:26:36 pm X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 912 CI works well for excimers and is equivalent to combination of charge transfer and excitation resonance. See, for example: "Photophysics of Polystyrene. 2. Pariser-Parr-Pople Studies of Excimer Structure" S. Blonski, K. Sienicki, and A. Herman Macromolecules 20 (1987) 329 and more recent references: "Excimer geometries in bichromophoric molecules: a theoretical and experimental study of 1,2-(bis-9-anthryl)-ethane" G.D. Scholes, K.P. Ghiggino, and G.J. Wilson Chemical Physics 155 (1991) 127 "Excimer interactions in poly(acenaphthalene) diads" D.G. Scholes and K.P. Ghiggino Chemical Physics Letters 188 (1992) 140 However, semi-empirical methods give good spectra or good geometries, but not both, and excited-state ab initio calculations seem to be too costly so far. I don't work on excimers now, but I am still very interested in the summary of responds to the excimer question. Slawomir Blonski From U6124673@ucsvc.ucs.unimelb.edu.au Tue Nov 23 01:49:51 1993 Received: from MUWAYB.UCS.UNIMELB.EDU.AU for U6124673@ucsvc.ucs.unimelb.edu.au by www.ccl.net (8.6.4/930601.1506) id BAA06481; Tue, 23 Nov 1993 01:45:40 -0500 From: Received: from hermes.ucs.unimelb.EDU.AU by muwayb.ucs.unimelb.edu.au (PMDF V4.2-14 #4399) id <01H5NW8VXTZK005K15@muwayb.ucs.unimelb.edu.au>; Tue, 23 Nov 1993 17:45:30 +1000 Received: from ucsvc.ucs.unimelb.edu.au by ucsvc.ucs.unimelb.edu.au (PMDF V4.2-14 #4399) id <01H5NVVQ59MC8WXRMI@ucsvc.ucs.unimelb.edu.au>; Tue, 23 Nov 1993 17:45:22 +1000 Date: Tue, 23 Nov 1993 17:45:22 +1000 Subject: Re: Excimer Calculations To: CHEMISTRY@ccl.net Message-id: <01H5NVVQ59ME8WXRMI@ucsvc.ucs.unimelb.edu.au> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Calculation of excimer emission wavelengths is a particularly non-trivial exercise. Ab initio calculations must employ extended basis sets and proper inclusion of correlation - the emission maximum shift with respect to that of the "monomer" should be fairly reliably calculated in this way, but not necessarily the actual maximum. For more practically-oriented calculations a modified version of QCFF/PI (used in e.g. G.D. Scholes, K.P. Ghiggino & G.J. Wilson, Chem. Phys., 155 (1991) 127) could be used. You may obtain that >from me (just e-mail me personally). Alternatively, what about CNDO/S/CI or INDO/S/CI - they should also give reasonable results? Regards Greg Scholes University of Melbourne From BALLY@CFRUNI52.bitnet Tue Nov 23 03:49:53 1993 Received: from CEARN.cern.ch for BALLY@CFRUNI52.bitnet by www.ccl.net (8.6.4/930601.1506) id DAA07067; Tue, 23 Nov 1993 03:04:16 -0500 Message-Id: <199311230804.DAA07067@www.ccl.net> Received: from CFRUNI52.BITNET by CEARN.cern.ch (IBM VM SMTP V2R2) with BSMTP id 9921; Tue, 23 Nov 93 09:02:12 SET Date: Tue, 23 Nov 93 09:02 N From: Subject: Re: Excimer calculations To: CHEMISTRY@ccl.net X-Original-To: INTERBITGATE%CHEMISTRY@ccl.net, BALLY Dear Netters, on his reply to the question concering calculation of excimer electronic structure, Greg Scholes suggested to try CNDO and/or INDO/S-CI. Although these procedures may look like an attractive choice, the one of them which I know personally (INDO/S-CI such as implemented for example in Zerner's ZINDO which is also offered in INSIGHT from Biosym) has one serious drawback which probably makes it useless for excimers: It absurdly overestimates through-space interactions at anything smaller than van der Waals distances. We have been trying to do calculations on pi-complex cations (which may be regarded as ionized excimers) and the splitting of the HOMO's and the LUMO's at distances between 2.8 and 3.0 Angstrom (as may be typical also for pi-excimers) were so large that the HOMO-LUMO-gap (or, conversely, the electronic transition corresponding to HOMO-LUMO excitation) was predicted in the IR! At larger distances, the picture becomes more realistic (for example, the splitting of the pi-states in dodecahedradiene, where two double bonds are held at a 3.5 Angstom distance is predicted to be 0.8 eV in excellent agreement with experiment). Of course all this boils down to the choice of the geometry, in particular the distance between the excimer components. We based our calculations on geometries obtained at a correlated ab-initio level which we assume to be reasonably realistic. Surely one could do an INDO/S calculation at some distance where experimental excimer emission wavelengths are predicted correctly but then the question poses itself whether we have gained any understanding by doing this calculation. I think the only procedure which is liable to give correct results without any fiddling is the CASPT2-model recently proposed by Roos et. al. and implemented in their program system MOLCAS 2. However, anything with more than about ten heavy atoms may take a lot of patience even with state-of-the art hardware and the program is not of the black-box type because some human intelligence is needed in the selection of the basis set and the active space for the MCSCF calculation. Therefore, I share the opinion of Greg Scholes that calculations of excimer emissions are a non-trivial issue, but I am also waiting eagerly to hear what other colleagues have to say on this matter thomas bally ------------------------------------------------------------------------------ | Prof. Thomas Bally | E-mail: BALLY@CFRUNI52 | | Institute for Physical Chemistry | | | University of Fribourg | Tel: 011-41-37 826 489 | | Perolles | FAX: 011-41-37 826 488 | | CH-1700 FRIBOURG | | | Switzerland | | ------------------------------------------------------------------------------ From noy@tci002.uibk.ac.at Tue Nov 23 05:49:54 1993 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id FAA07792; Tue, 23 Nov 1993 05:02:18 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA02812 (5.65c/IDA-1.4.4 for ); Tue, 23 Nov 1993 11:01:32 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA12854; Tue, 23 Nov 1993 11:01:28 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9311231001.AA12854@tci002.uibk.ac.at> Subject: Molecular Dynamics questions To: chemistry@ccl.net Date: Tue, 23 Nov 1993 11:01:26 +0100 (NFT) Cc: chem-comp@mailbase.ac.uk X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 830 Dear CCL fellows, I am writing an MD program and here comes some questions. To my experience, the average temperature tends to raise up gradually in a simulation resulting in the increasing of total energy. 1) Is it possible to apply a "scaling temperature" algorithm to control the temperature range ( my MD is NVE ) ? To my idea, scaling the velocities cause the deviation of the p-q coordinate ( generalized momentum-generalized coordinates ) in the phase space. The trajectories are therefore deviated, is it true ? How to scale both velocities and coordinates to keep the correct trajectories and p-q coordinates in the phase space ? 2) Is it possible to apply an "external bath" in which is generally used with NVT ensemble to an NVE ensemble ? Thanks a lot in advance. best wishes, T.K.Noy From JEREMYW@num-alg-grp.co.uk Tue Nov 23 08:49:59 1993 Received: from ben.britain.eu.net for JEREMYW@num-alg-grp.co.uk by www.ccl.net (8.6.4/930601.1506) id IAA09139; Tue, 23 Nov 1993 08:39:38 -0500 Received: from num-alg-grp.co.uk by ben.britain.eu.net via JANET with NIFTP (PP) id ; Tue, 23 Nov 1993 13:16:35 +0000 Message-Id: <25371.9311231313@nags2.nag.co.uk> Received: from vax.nag.co.uk (nagvax) by nags2.nag.co.uk (4.1/UK-2.1) id AA25371; Tue, 23 Nov 93 13:13:56 GMT Date: 23 Nov 93 13:11:00 WET From: JEREMY WALTON Subject: Molecular Dynamics answers To: CHEMISTRY Hi Noy, >> 1) Is it possible to apply a "scaling temperature" algorithm >>to control the temperature range ( my MD is NVE ) ? To my idea, >>scaling the velocities cause the deviation of the p-q coordinate >>( generalized momentum-generalized coordinates ) in the phase space. >>The trajectories are therefore deviated, is it true ? How to scale >>both velocities and coordinates to keep the correct trajectories and >>p-q coordinates in the phase space ? The traditional way to get the NVE simulation running at (close to) the temperature you want is to have an equilibration period where the velocities are all uniformly scaled so the system is forced to have the kinetic energy appropriate to the required temperature. Following this period (typically a few thousand timesteps), scaling is switched off and the averaging over configurations can be started. The temperature should be monitored during this averaging period (it's one of the things you calculate as an average); if it drifts too much, then maybe the equilibration period wasn't long enough, or maybe your timestep is too big. >> 2) Is it possible to apply an "external bath" in which is >>generally used with NVT ensemble to an NVE ensemble ? There are a number of algorithms for this. Two which I recall are that of Berendsen and that of Nose. Check out Allen & Tildesley's "Computer Simulation of Liquids" (OUP, 1987), where all this is described in some detail. Hope this helps, Jeremy -------------------------------------------------------------------------------- | Jeremy Walton nagjpw@vax.oxford.ac.uk | | The Numerical Algorithms Group Ltd, Oxford, UK jeremyw@nag.co.uk | | Tel: +44 865 511245 | | Fax: +44 865 310139 | -------------------------------------------------------------------------------- From ravishan@swan.wcc.wesleyan.edu Tue Nov 23 08:57:02 1993 Received: from swan.wcc.wesleyan.edu for ravishan@swan.wcc.wesleyan.edu by www.ccl.net (8.6.4/930601.1506) id IAA09145; Tue, 23 Nov 1993 08:40:19 -0500 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA21821; Tue, 23 Nov 1993 08:37:35 -0500 Date: Tue, 23 Nov 1993 08:37:35 -0500 Message-Id: <9311231337.AA21821@swan.wcc.wesleyan.edu> From: "G. Ravishanker" Sender: ravishan@swan.wcc.wesleyan.edu To: chemistry@ccl.net Subject: Improper dihedrals in GROMOS This is a question regarding the improper dihedral parameters for the side chains of two amino acids, VAL and LEU, as it appears in the GROMOS parameter files. The residue topology file lists an entry for the following improper dihedral angles: VAL: CB CG1 CG2 CA LEU: CG CD1 CD2 CB The force constants for both these are 80 kcal/mol-1/rad-2 and the equilibrium angle is 35.264. In VAL, CG1 and CG2, and in LEU, CD1 and CD2 are identical united atom CH3's. However, it is clear that the improper dihedral angle measured depends on the order of the atoms CG1 and CG2 for VAL and CD1 and CD2 for LEU. We have noticed that the order of CG1 and CG2 (and CD1 and CD2) as they appear in PDB files give improper dihedrals that are in the neighbourhood of -30. As a result, during the course of energy minimization or early MD, this dihedral angle gets flipped to around +30, significantly altering the side chain geometry, energetics and subsequently the backbone geometry. The solutions to this problem are rather simple: 1. Switch the CG1 and CG2 in VAL and CD1 and CD2 in LEU before generating the binary topology file. 2. Change the GROMOS RTF files to reflect the correct improper order. We are interested in knowing whether other GROMOS users have encountered this problem, or whether this is mentioned anywhere in the GROMOS manual. We have checked the RTF files for GROMOS86 as well as GROMOS87 and both contain the same ordering. In all trial runs we notice that the improper dihedral flips almost immediately and that in the specific case of lysozyme, the backbone RMS difference between the incorrect and correct ordering can be as much as .5A within 50ps (which is considerable). In some other cases, we notice that this does not have too much of an effect. It is all a function of how many VAL and LEU the protein has. Any comments and/or clarifications are appreciated. Bill Harte, Bristol-Myers Squibb Pharmaceutical Research Institute G. Ravishanker, Dept. of Chemistry, Wesleyan University. **************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06457. * **************************************************************************** From J_BROWN@uvmvax.uvm.edu Tue Nov 23 09:50:00 1993 Received: from uvmvax for J_BROWN@uvmvax.uvm.edu by www.ccl.net (8.6.4/930601.1506) id JAA09563; Tue, 23 Nov 1993 09:08:01 -0500 From: Received: from uvmvax.uvm.edu by uvmvax.uvm.edu (PMDF #12059) id <01H5NE30PW7K0056RX@uvmvax.uvm.edu>; Tue, 23 Nov 1993 09:05 EST Date: Tue, 23 Nov 1993 09:05 EST Subject: Response to MD with variable temp question To: chemistry@ccl.net Message-id: <01H5NE30PW7K0056RX@uvmvax.uvm.edu> X-VMS-To: IN%"chemistry@ccl.net" K. T. Noy writes: > Subj: Molecular Dynamics questions > Dear CCL fellows, > I am writing an MD program and here comes some questions. > To my experience, the average temperature tends to raise > up gradually in a simulation resulting in the increasing of total > energy. > 1) Is it possible to apply a "scaling temperature" algorithm > to control the temperature range ( my MD is NVE ) > Thanks a lot in advance. > best wishes, > T.K.Noy -------------------------------------------------------------------- I have a comment that is a "tangental" answer. In fitting several variable temperature NMR simulations where you have an equilbrium situation between several species of various populations, I noted that I could not obtain satisfactory fits of my spectra by simply increasing the rate of exchange between the various species (as dictated by the Eyring equation) until I began to increase the populations of the minor species with increasing temperature. Further, the best fits were obtained when I could track the popolations of each species at several temperatures and generate a Van't Hoff plot that could be used to "predict" the populations for spectra where overlap prevented population elucidation. If your MD model is varying in temperature, a more realistic model would include an increasing of minor conformation populations with increasing temperature (as dictated by the Van't Hoff equation). What do others think. Jay Brown From system@alchemy.chem.utoronto.ca Tue Nov 23 10:02:55 1993 Received: from alchemy.chem.utoronto.ca for system@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id IAA09258; Tue, 23 Nov 1993 08:56:26 -0500 Received: by alchemy.chem.utoronto.ca (5.65/1.34) id AA03985; Tue, 23 Nov 93 08:55:56 -0500 Date: Tue, 23 Nov 93 08:55:56 -0500 From: system@alchemy.chem.utoronto.ca (System Admin (Mike Peterson)) Message-Id: <9311231355.AA03985@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Re: MOPAC7 port to an RS/6000 I finally got MOPAC 93 (the licensed version of MOPAC 7) to work on our HP-UX (9.01) and Domain/OS (SR10.4) systems, but many changes were required. Here is the text summary of what I did; I will send the complete context diff patches to anyone who asks. I am somewhat surprised that these changes have not propagated back to QCPE by now since I sent them in 2 months ago. CHANGES TO MOPAC 93 =================== Version: 1993/09/18. The following changes were made to MOPAC 93 (version 93.00) to allow it to run corectly on HP 7xx series systems running HP-UX 9.01 and HP/Apollo Domain/OS DN10000 systems. Even with these changes, the 'mopac_examples/testall.dat' data set still fails test cases 1-3 and 6 (they are labelled as "Ethylene" but are in fact HCNH+). Special notes: *_source/Makefile: It is essential that MOPAC be compiled with static data storage (so that all subroutine local variables are SAVEd between calls), as opposed to using the "stack" (or dynamic data storage). Doing this also automatically zeroes all undefined variables on the HP, and this is recommended for all systems. Many routines have SAVE statements in them, but MOPAC does not work properly with just those statements. Some Makefile's have features in them which do not work with the version of make distributed with many systems; the fancy stuff has been replaced with regular commands. Recursive Makefiles changed to allow environment variables to be recovered (change ' to " in the 'make' command). bz_source/orient.f: It is illegal to read CHARACTER data with '*' format unless the character strings are surrounded by ' characters in the input file. The program was changed to scan for the TITLE after reading the INTEGER/REAL values with '*'. bz_source/tkhard.f, density_source/tkhard.f: This routine creates a Tektronix 4010 graphics file, which can either be displayed on a PC running MS-KERMIT, or printed directly on a Imagen laser printer, or converted to PostScript with 'tek2ps'. mopac_source/ef.f, mopac_source/flepo.f, mopac_source/nllsq.f, mopac_source/powsq.f, mopac_source/wrtkey.f: Changed timing data formats since machines are so fast that timing resolution down to ten of milliseconds is required to run many of the test cases. mopac_source/calpar.f: The DO 40 loop doesn't go over element 102 (Cb), so the correction made to the source code may be incorrect (at least it now produces the same output as the original Sun version). mopac_source/drc.f: '*' format for long strings is not consistent across platforms, and results in 2 lines of titles on some systems. mopac_source/esp.for: Routine ELESP does two OPENs on the ESP data output file; the second one fails since it tries to open a scratch file as "NEW" which is illegal. mopac_source/repp.f: This routine divides by zero for capped bonds, which aborts the job on some systems and does lots of arithmetic with NaN/INF values on others; the code was modified to return all zeroes when this case was detected, but this may not be the correct action to take. mopac_source/second.f: Attempts to REWIND unit 4 before OPEN; the REWIND was moved inside the OPEN/CLOSE. mopac_source/wrtkey.f: The values for "T=" and "DUMP=" are not reset to a default value at the start of a new calculation, but are set to the time left from the last calculation, and the last specified DUMP value respectively; this is not documented in the manual, and nothing has been done by me to correct the situation, if it should be corrected since this seems to be the historical behaviour. The code to remove DEBUG keywords has been modified since the DEBUG keywords are not printed in the output file if this is done, and the removal was done in a way where either all of the keywords would be removed, or just until the first one was found, with the difference due to the vendor's FORTRAN implementation and optimization level used. mopac_examples/port.dat, mopac_examples/testall.dat: Many timing changes made for "restart" jobs to work properly; MOPAC desparately needs a facility to kill the job after a specific number of iterations, so that test jobs can be made machine-independent. Mike. From tharvey@pip.oci.utoronto.ca Tue Nov 23 11:51:14 1993 Received: from gpu.utcc.utoronto.ca for tharvey@pip.oci.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id KAA10340; Tue, 23 Nov 1993 10:50:40 -0500 Received: from pip.oci.utoronto.ca ([128.100.195.8]) by gpu.utcc.utoronto.ca with SMTP id <18890>; Tue, 23 Nov 1993 10:50:36 -0500 Received: from kobun.oci.utoronto.ca by pip.oci.utoronto.ca (4.1/SMI-4.1) id AA11896; Tue, 23 Nov 93 10:42:27 EST Date: Tue, 23 Nov 1993 10:42:27 -0500 From: tharvey@pip.oci.utoronto.ca (Tim Harvey) Message-Id: <9311231542.AA11896@pip.oci.utoronto.ca> To: CHEMISTRY@ccl.net Subject: Re: Improper dihedrals in GROMOS I think it's been known for a long time (almost since it was actually created) that the GROMOS definition is opposite to IUPAC. It is mentioned in the GROMOS manual; section 4.2. Obviously having the Leu and Val chiral carbons invert during a run is going to have significant effects. Tim, who checks every line in GROMOS topology files by hand. From herbert.homeier@rchs1.chemie.uni-regensburg.de Tue Nov 23 12:03:49 1993 Received: from rrzs1.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id LAA10596; Tue, 23 Nov 1993 11:11:33 -0500 Received: from rchs1.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA12108; Tue, 23 Nov 93 17:11:08 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.31)) id AA01778; Tue, 23 Nov 93 17:12:00 +0100 Date: Tue, 23 Nov 93 17:12:00 +0100 From: Herbert Homeier (t4720) Message-Id: <9311231612.AA01778@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Extended Hueckel parameters Cc: savary@sc2a.unige.ch Hi, I think that the following question which I found in some news group should be posed to the Computational Chemistry List: Herbert In article 29563@news.unige.ch, savary@sc2a.unige.ch () writes: > Hi there over the net, > > Does someone know the existence of table of data containing > all the parameters for extended Hueckel calculations; > that is : > - standard Hii's (valence ionization potentials) > - slater exponents and coefficents > - charge iteration parameters (that part is the more important) > > I already have the table of parameters, collected by Santiago Alvarez, > from Barcolena. But a few of those parameters seem not so correct, in particular > for the charge iteration parameters. > > > Hope to hear soon from you > > Francois Savary, University of Geneva, Department of Physical Chemistry > 30, quai E. Ansermet, CH-1211 Geneva 4 > +4122 702 65 32 (phone) +4122 702 65 18 (fax) > savary@sc2a.unige.ch (e-mail) ----------------- Herbert.Homeier@rchs1.chemie.uni-regensburg.de From rovshan@atlas.chemistry.uakron.edu Tue Nov 23 12:52:33 1993 Received: from dax.cc.uakron.edu for rovshan@atlas.chemistry.uakron.edu by www.ccl.net (8.6.4/930601.1506) id MAA12025; Tue, 23 Nov 1993 12:40:06 -0500 Received: from atlas.chemistry.uakron.edu by dax.cc.uakron.edu (5.65/Ultrix4.3) id AA20232; Tue, 23 Nov 1993 12:39:56 -0500 Received: from cronus.chemistry.uakron.edu by atlas.chemistry.uakron.edu (4.1/SMI-4.1) id AA08028; Tue, 23 Nov 93 12:43:15 EST Date: Tue, 23 Nov 93 12:43:15 EST From: rovshan@atlas.chemistry.uakron.edu (Rovshan G. Sadygov) Message-Id: <9311231743.AA08028@atlas.chemistry.uakron.edu> To: CHEMISTRY@ccl.net Subject: Excimer details Hellow Dear Netters, Yesterday I posted a quiestion about excimer calculations. Thanks for interest it brought about from some of you. People asked about details of calculations and objectives. They are following; I want to calculate excimer states of naphthalene dimer in parallel conformation using supermolecule model of dimer. I need to find out dependence of total energy of supermolecule on interplanar distance between naphthalene monomers. Excited state of supermolecule corressponding to HOMO->LUMO transition supposedly forms bound state at interplanar distance 3.3 - 3.5 A. I also need to calculate second excited state of supermolecule. This state is expected to be nonbonding, laying about 2.0 ev above excimer state at bonding conformation of latter and approaching it at large interplanar distances. I have now a problem somehow close to one described by Dr T Bally in his E-mail reply. According to Argus INDO1/s calcualtions ground state of supermolecule is not repulsive at interplanar distances 2.0 - 3.0 A. As a matter of fact it is attractive(!!!). MOPAC5 with AM1 Hamiltonian yields quite resonable results for ground state of supermolecule. It predicts vdWaals bonding at 5.5 A interplnar distance and repulsive ground state at interplanar distance shorter than 4.0 A. The second problem with Argus is that at short interplanar distances molecular orbital carrying LUMO features (which is antibonding) becomes an occupied molecular orbital in ground state. And conversely, MO corresponding to HOMO of monomer becomes unoccypied MO. It is true for MOPAC5 AM1 too. So these are problems I currently encounter in excimer calculations. I'll be glad to provide more details if needed. Thanks in advance to all who are interested. Rovshan G Sadygov. From jkl@ccl.net Tue Nov 23 13:04:15 1993 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id MAA11469; Tue, 23 Nov 1993 12:04:01 -0500 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id MAA09239; Tue, 23 Nov 1993 12:03:59 -0500 Date: Tue, 23 Nov 1993 12:03:59 -0500 Message-Id: <199311231703.MAA09239@krakow.ccl.net> To: chemistry@ccl.net Subject: AIX sendmail is DANGEROUS !!! Cc: jkl@ccl.net, vazquez@iqm.unicamp.br Dear Netters, Pedro Vazquez agreed to share some comments on sendmail vulnerability with AIX. I do not quote the prescription on how to use sendmail to do ANYTHING with ROOT priviledges on the RS/6000 under AIX to protect the innocent (you do not need to know this, do you?). However you should replace the sendmail which you have now with a new version (8.6.4). Moreover, the way to use a sendmail bug to break into your machine was widely publicized on the Usened. So beware, jerks may know about it... If you need more info, contact Pedro directly. Some comments from Pedro: From: Pedro A M Vazquez >Dear Jan: > I've just mailed the message below to the CERT people (...) > I think all AIX users may be in danger, many of the our list coleagues > use AIX machines but do not receive CERT reports (...) > I have compiled sendmail 8.6.4 for AIX machines and I can make it availble > in binary form for anonymous ftp. >Regards >Pedro Thanks again Pedro for all your help... Jan jkl@ccl.net From kukh@icph28.sherna.msk.su Tue Nov 23 13:50:00 1993 Received: from moscvax.demos.su for kukh@icph28.sherna.msk.su by www.ccl.net (8.6.4/930601.1506) id NAA12750; Tue, 23 Nov 1993 13:25:51 -0500 Received: by moscvax.demos.su id AA03157 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Tue, 23 Nov 1993 21:25:45 +0300 Received: by kremvax.demos.su; Tue, 23 Nov 1993 21:13:05 +0300 Received: by phreak.ex952.demos.su; Tue, 23 Nov 1993 20:30:49 +0300 Received: by icph.sherna.msk.su; Tue, 23 Nov 93 19:11:48 +0300 (MSK) Received: by icph28.sherna.msk.su (UUPC/@ v5.09gamma, 14Mar93); Tue, 23 Nov 1993 19:11:01 +0300 To: chemistry@ccl.net Message-Id: Organization: Inst. of Chem.Phys. Russia Acad. of Sci. From: kukh@icph28.sherna.msk.su (Dr. Serge V. Kukharenko) Date: Tue, 23 Nov 93 19:10:59 +0300 (MSK) Return-Receipt-To: kukh@icph.sherna.msk.su X-Mailer: dMail (Demos Mail v1.13a) Subject: Transition metal pi-complexes calculation request Lines: 28 Dear Netters: Does anybody know about possibility to perform quantum chemical calculation (HOMO/LUMO energy, molecular dynamics, etc.) of transition metal sandwich and half-sandwich pi-complexes (like ferrocene or cymantrene) with condensed polyaromatic ligands (e.g. naphtalene, indenyl, fluorenyl)? I realise that it is very complicated problem. Furthermore, I have only a minor experience with calculation (PC Model and HyperChem only). May be somebody is interested in performance of above calculations and scientific collaboration with me? I've obtained very interesting and unusual experimental results on chemistry of the titled complexes and can send it upon your request. Please respond to me via e-mail, I can summarize answers to the list. ----------------------------------------------- Dr. Serge Kukharenko Department of Kinetics and Catalysis Institute of Chemical Physics in Chernogolovka Russia Academy of Science Moscow Region Chernogolovka 142432 Russia e-mail: kukh@icph.sherna.msk.su ----------------------------------------------- From shenkin@still3.chem.columbia.edu Tue Nov 23 14:51:16 1993 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.4/930601.1506) id OAA13407; Tue, 23 Nov 1993 14:11:26 -0500 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA06504 (5.65c+CU/IDA-1.4.4/HLK for jkl@ccl.net); Tue, 23 Nov 1993 14:11:22 -0500 Received: by still3.chem.columbia.edu (930416.SGI/930416.SGI.AUTO) for @cunixf.cc.columbia.edu:chemistry@ccl.net id AA12549; Tue, 23 Nov 93 14:11:06 -0500 Date: Tue, 23 Nov 93 14:11:06 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9311231911.AA12549@still3.chem.columbia.edu> To: Jan Labanowski , chemistry@ccl.net Subject: Re: AIX sendmail is DANGEROUS !!! Cc: vazquez@iqm.unicamp.br, jkl@ccl.net > From: Jan Labanowski > > Dear Netters, > Pedro Vazquez agreed to share some comments on sendmail vulnerability > with AIX. ..... About two weeks ago CERT issued an advisory to the effect that virtually all vendors' sendmails are vulnerable, so this is not news. CERT proposed several workarounds; please see their advisory for details. In addition, several vendors (SGI, for example; I don't know about IBM) have made new versions of sendmail available, in some cases by anonymous ftp. There was another, similar advisory about the xterm program. Bottom line: unless you have reason to believe otherwise, assume that your sendmail and xterm programs pose security threats. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ********************** Atheist: an evangelical agnostic. ******************** From mercie@med.cornell.edu Tue Nov 23 19:50:04 1993 Received: from cumc.cornell.edu for mercie@med.cornell.edu by www.ccl.net (8.6.4/930601.1506) id TAA15796; Tue, 23 Nov 1993 19:12:58 -0500 Received: from localhost (mercie@localhost) by cumc.cornell.edu (8.6.4/ECH1.13) id TAA15118; Tue, 23 Nov 1993 19:11:32 -0500 Date: Tue, 23 Nov 1993 19:09:14 -0500 (EST) From: Gustavo Mercier Subject: honod 8.4 in sgi To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="0-7879-754099891:#15092" --0-7879-754099891:#15092 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Netters! I have included an attachment about my experience porting hondo 8.4 as provided in Chem-Station into a INDIGO R4000 running IRIX 4.0.5F. I hope this is useful! I am able to reproduce the examples as reported in the documentation. good luck gus mercier mercie@cumc.cornell.edu --0-7879-754099891:#15092 Content-Type: TEXT/PLAIN; charset=US-ASCII; name="hondo8.inSGI" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: bW9kaWZpY2F0aW9uIDE6CklTSU5HTCA9IDIgZm9yIDMyIGJpdCBtYWNoaW5l ClZFQ1RPUiA9IC5GQUxTRS4KCWZpbGVzIGFmZmVjdGVkCmN0bC5mCmNvbW1l bnQ6IHNlZSBkb2N1bWVudGF0aW9uCiMjIyMKbW9kaWZpY2F0aW9uIDI6CmV4 Y2x1ZGVkIGZpbGUgZnJvbSBsb2FkaW5nIHBoYXNlOgoJZmlsZXMgYWZmZWN0 ZWQ6CnZlYy5mCmNvbW1lbnQ6IHNlZSBkb2N1bWVudGF0aW9uCiMjIyMKbW9k aWZpY2F0aW9uIDM6CmFwcGxpZWQgIjEsJHMvQFBST0NFU1MvYyBAUFJPQ0VT Uy9nIiB0byBjb21tZW50IG91dCB0aGUgbGluZXMgdXNpbmcgdmkgZWRpdG9y CglmaWxlcyBhZmZlY3RlZCB3aXRoIG51bWJlciBvZiBpbnN0YW5jZXMgdGhh dCB0aGUgY2hhbmdlIGFwcGxpZWQ6CmN0bC5mOjYKY2kxLmY6MwpjaTIuZjoz CmRlci5mOjIKaHNzLmY6NQppbnQuZjozCm1wMi5mOjE1Cm1wNC5mOjYKbnRu LmY6MgpzY2YuZjo4CiMjIyMKbW9kaWZpY2F0aW9uIDM6CnJlbmFtZWQgdGhl 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