From robert@pauli.utmb.edu Mon Dec 1 12:38:34 1997 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.8.3/950822.1) id LAA11772; Mon, 1 Dec 1997 11:51:07 -0500 (EST) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA01490; Mon, 1 Dec 97 10:54:11 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SUN.8.6.12/950213.SUN.AUTOCF) id KAA21370; Mon, 1 Dec 1997 10:51:43 -0600 From: "Robert Fraczkiewicz" Message-Id: <9712011051.ZM21369@pauli.utmb.edu> Date: Mon, 1 Dec 1997 10:51:43 -0600 In-Reply-To: "CCL:normal mode force constant" (Nov 27, 11:09am) References: <9711271009.AA18731@anne.chemie.unibas.ch> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: , chemistry@www.ccl.net Subject: Re: CCL:normal mode force constant Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Frederique, > I would like to get the normal mode force constant for each bond of a molecule > to use them in the equation of Marcus theory. I do not know how to calculate > the normal mode force constant for a bond. I would be pleased if somebody > could help me to solve this problem. > > Thank you. > > Frederique I assume that you are interested in a harmonic force field. Normally, you need to do elaborate ab initio calculations to get good force constants. But if you have a good set of experimental data (IR, Raman; the more isotopomers, the better), then you can use RAMVIB to quickly fit force constants to observed vibrational frequencies. Usually, the quality of fit will be much better than that from ab initio. However, assignments and force constant selection will be the hard part. RAMVIB has some auxilliary programs to make it easier. It is available free of charge to academic users at CCL archives: ftp://www.ccl.net/pub/chemistry/software/SGI/ramvib/ Best regards, Robert Fraczkiewicz University of Texas Medical Branch Galveston, TX 77555 From wolfgang@sindbad.anorg.chemie.tu-muenchen.de Mon Dec 1 13:41:53 1997 Received: from sindbad.anorg.chemie.tu-muenchen.de for wolfgang@sindbad.anorg.chemie.tu-muenchen.de by www.ccl.net (8.8.3/950822.1) id NAA12087; Mon, 1 Dec 1997 13:14:33 -0500 (EST) From: Received: from localhost by sindbad.anorg.chemie.tu-muenchen.de; (5.65v3.2/1.1.8.2/11Oct96-0330PM) id AA01880; Mon, 1 Dec 1997 19:13:50 +0100 Message-Id: <9712011813.AA01880@sindbad.anorg.chemie.tu-muenchen.de> To: CHEMISTRY@www.ccl.net Cc: dieter@schlaubi.anorg.chemie.tu-muenchen.de Subject: Turbomole on SGI O2 Date: Mon, 01 Dec 97 19:13:49 +0100 X-Mts: smtp Dear CCLers: Does anyone of you have experience running Turbomole on an O2? I haven't been successful in running Turbomole (Insight/Discover Environment) on my SGI O2 (180 MHz, 128 MB) correctly. The program produces several errors, e.g., energies such as -100.3470 are written as -100,0000 (note the comma!) to the archive file, convergence limits are strange in the same way when written to the control file, etc. With release 95.0, restarting a previous run after editing the control file allowed optimization, but not frequency calculations. With release 97.0, optimization as well as frequency calculations can be performed without editing the control file, but the density convergence deviation is then set to zero (which leads to slow SCF convergence). Test jobs on a different O2 with Release 95.0 haven't shown problems with optimization, but with frequency calculations. Therefore my questions: - Does anyone of you have similar problems? - If yes, can you tell me if the error is due to the software or the hardware ? Please reply to dieter@schlaubi.anorg.chemie.tu-muenchen.de. I will summarize. Thanks to all, Dieter Gleich From 94970459@tolka.dcu.ie Mon Dec 1 17:38:36 1997 Received: from tolka.dcu.ie for 94970459@tolka.dcu.ie by www.ccl.net (8.8.3/950822.1) id RAA13763; Mon, 1 Dec 1997 17:07:41 -0500 (EST) Received: by tolka.dcu.ie (5.65v4.0/1.1.8.2/14Feb96-0535PM) id AA03606; Mon, 1 Dec 1997 22:03:35 GMT Date: Mon, 1 Dec 1997 22:03:35 +0000 (GMT) From: Paddy Kane <94970459@tolka.dcu.ie> To: HChem Supp , HChem User , CCL Every , Darren Fayne <95970665@tolka.dcu.ie> Subject: HyperChem: Incorrect geometries in amines Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am a user of HyperChem, version 4. Whenever I use molecular mechanics with the MM+ force field, to geometry optimise molecules such as Phenylamine (C6H5NH2), the geometry about the N atom is planar rather than pyramidal, i.e., an atom type of N2 is used for the nitrogen atom, rather than N3 as would be expected. I get the same result with molecules such as H2C=CHNH2 or H2C=NNH2. I also get incorrect geometries if I initially use the model builder to obtain an approximate geometry for such molecule or if I use any of the other three force fields available within HyperChem. If I initially set the atom type for the nitrogen atom to be N3, I still get an planar geometry about the nitrogen atom. However, for molecules such as methylamine and cyclohexamine, i.e., where the atom bonded to the nitrogen atom is saturated, the correct geometry and atom type are obtained for the nitrogen atom. Has anyone else experienced this problem? I would be very grateful if someone could advise me of how to solve the problem. Kind rgds, Paddy. ************************************************************************* * * * Paddy Kane email: 94970459@tolka.dcu.ie * * School of Chemical Sciences * * Dublin City University Tel: 00-353-1-7045641 * * Dublin 9 * * Ireland. Fax: 00-353-1-7045503 * * * ************************************************************************* From glossman@overnet.com.ar Wed Nov 26 08:37:29 1997 Received: from carpincho.overnet.com.ar for glossman@overnet.com.ar by www.ccl.net (8.8.3/950822.1) id IAA16670; Wed, 26 Nov 1997 08:34:11 -0500 (EST) Received: from nppp229.overnet.com.ar (nppp229.overnet.com.ar [200.16.164.242]) by carpincho.overnet.com.ar (8.8.8/8.8.5) with SMTP id KAA17561 for ; Wed, 26 Nov 1997 10:34:36 -0300 Message-Id: <3.0.1.16.19971126102806.10df4d70@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar (Unverified) X-Mailer: Windows Eudora Light Version 3.0.1 (16) Date: Wed, 26 Nov 1997 10:28:06 To: chemistry@www.ccl.net From: "Dr. M. Daniel Glossman" Subject: programs for plotting densities Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters: I would like to receive information about any software (commercial or not) for the Windows NT environment that could be useful for plotting two and three dimensional electon densities and electrostatic potentials starting from Gaussian 94 computed wavefunctions ( .out and .chk files). I thank you in advance for your answers. Daniel Glossman ****************************************************************************** Dr. M. Daniel Glossman Universidad Nacional de Lujan e-mail: glossman@overnet.com.ar Departamento de Ciencias Basicas Phone: (+54) 323 23171 Casilla de Correo 221 FAX: (+54) 323 25795 (6700) Lujan Republica Argentina From kristyan@euch4e.chem.emory.edu Wed Nov 26 10:42:15 1997 Received: from euch4e.chem.emory.edu for kristyan@euch4e.chem.emory.edu by www.ccl.net (8.8.3/950822.1) id KAA17131; Wed, 26 Nov 1997 10:02:35 -0500 (EST) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA22707; Wed, 26 Nov 1997 10:02:37 -0500 Date: Wed, 26 Nov 1997 10:02:37 -0500 Message-Id: <9711261502.AA22707@euch4e.chem.emory.edu> To: chemistry@www.ccl.net Dear Collagues I read: >I am wondering if computational >chemistry is overlooked by the Nobel prize committee. I am sure they know about it, unfortunately (or fortunatrly) more pople are qualified for Nobel prize than those who are awarded. With this respect the life is - as in many cases - unfear. What we should worry about and speak up is to get more money for basic research. (For example with a non science major B.S. degree it is much easier to get a job than with a Ph.D. in (certain) sciences, and the requirements are even stronger to graduate in those programs, etc., etc.) kristyan@euch4e.chem.emory.edu Sandor Kristyan November 25, 1997 From schrecke@t12.lanl.gov Wed Nov 26 17:37:32 1997 Received: from mailhost.lanl.gov for schrecke@t12.lanl.gov by www.ccl.net (8.8.3/950822.1) id RAA20026; Wed, 26 Nov 1997 17:27:18 -0500 (EST) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.8.8/(cic-5, 10/28/97)) with SMTP id PAA25466 for ; Wed, 26 Nov 1997 15:27:14 -0700 (MST) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Nov 1997 15:30:43 -0700 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: Summary: atomic symmetry in G94 Dear CCL readers, here is my summary on the atomic symmetry in G94 and related issues. I got a number of interesting replies that are listed below. Eventually, I solved my problem by simply refraining from using very diffuse basis functions on Fe -- the Fe+ case should, indeed, give 5 equivalent d orbitals as it has a half-filled shell. The suggestion of first running a lower basis set to build the guess (Brian Teppen) is also useful, and I have done just that in a number of other cases. Finally, I have also posted this summary at http://www.t12.lanl.gov/~schrecke/research.DIR/CCL_G94Atoms.html Thanx again to everyone who took the time to reply! A Happy Thanksgiving to all of us in America and elsewhere! Best regards, Georg --------------------------------------------------- Original question: I am trying to run a few atoms or ions (e.g., Fe_+) in Gaussian 94, restricted open shell. My incentive is to compare orbital energies as they come out of different methods and / or basis sets. Now, when I run such an atom, the program turns off symmetry. This would not bother me too much if the subsequent SCF had not mixed up states. However, it does so, and I do not get, for instance, 5 degenerate d orbitals of the same energy. I tried to enforce some symmetry by placing other nuclei into symmetric positions far away but then I run into SCF convergence problems. Any advice or tricks? Best regards, Georg --------------------------------------------------- Date: Fri, 21 Nov 1997 11:47:35 -0600 From: "Vitaly A. Rassolov" Dear Georg, As far as I know, there is no way to solve your problem within Gaussian package. This was the original philosophy of Gaussian creators: stay away from symmetry in favor of the lower energy. Gaussian is an extreme case, but I don't know any other molecular program which can enforce proper atomic symmetry (although they usually don't mix the symmetry they have during SCF iterations). [Comment of GS: ADF does allow the use of the full atomic symmetry, or of any lower symmetry as desired.] Fe+ is, of course, an exception with its half-filled d-shell. It should be similar to Mn, which does give me five identical d orbitals, even on the UHF level (since the lowest energy configuration is symmetric). You only have to make sure you converge to the true minimum by using "stable=opt" option. [Comment of GS: I don't get the "stable=opt" option to work with my restricted calculation, B3LYP in this case. An unresticted calculation seems to give the proper five d orbitals, even without the "stable" keyword.] When I need proper atomic symmetry, I use ATOMSCF program by B. Ross & Co. from the 60's. If you find out how to force Gaussian to give identical d orbitals for not spherically symmetric atoms, please share your information on CCL. I know couple other people who would like to know it. Best wishes, Vitaly Rassolov Department of Chemistry tel. (847) 491-3423 Northwestern University 2145 Sheridan Rd. rassolov@chem.nwu.edu Evanston, IL 60208-3113 --------------------------------------------------- Date: Fri, 21 Nov 1997 21:06:27 -0800 From: "Ananikov V.P." Dear Georg, As I know, it is possible to use high symmetry groups for single atoms/ions (up to d2h) only if the starting electron density is symmetric. For Fe+ you should choose C1 group, otherwise d electrons might be nonequivalent at the end of your calculations. You can try MCSCF and C1 group for Fe+, it seems it works with GAMESS(I am not sure ;-). If you do not have GAMESS near at hand, let me know. Of course, I am interesting in your summary. Good luck! Valentin. Valentin P. Ananikov NMR Laboratory N.D. Zelinsky Institute of Organic Chemistry Leninsky Prospect 47 Moscow 117913, Russia e-mail: val@nmr1.ioc.ac.ru http://nmr1.ioc.ac.ru/Staff/AnanikovVP/ Fax (7095) 1355328 Phone (7095) 9383536, (7095) 1359094 --------------------------------------------------- Date: Fri, 21 Nov 1997 20:37:58 +0100 (MET) From: "Dr. Alexei Arbouznikov" Dear Georg, Unfortunately, if you use restricted Hartree-Fock within the Gaussian program, you can not get the correct degeneracy of the open shells, except for the simplest case of exactly half-filled open shells (try, e.g., Mn++ ion - d5 configuration, and you will obtain 5 degenerate d-orbitals). To get the correct degeneracy in some more complicated configurations (non-half-filled one open shell or several open shells, e.g., 3d and 4s with occupation numbers other than 1/2 for at least one of them), you have to use GVB(0) option in the Gaussian, and specify explicitely the vector coupling coefficients for the desired state (the way to do it should be indicated in the G94 manual). Other solution of this problem is using another ab initio programs with well-elaborated ROHF techniques, such as, e.g., Monstergauss-92. If you are interested in, please, ask some additional questions. Best regards, Dr. Alexei Arbouznikov Ecole Nationale Superieure de Chimie, Laboratoire de Materiaux Catalytiques et Catalyse en Chimie Organique, UMR 5618 CNRS-ENSCM - Prof. F.Fajula, 8, rue de l'Ecole Normale 34296 Montpellier, Cedex 5 FRANCE Telephone: (33) 4-67-14-72-68 Fax: (33) 4-67-14-43-49 E-mail: alexei@palladium.enscm.fr --------------------------------------------------- From: Anatoli Korkin Date: Fri, 21 Nov 1997 14:13:28 -0700 (MST) Georg, Send me an input example to korkin@qtp.ufl.edu and I will check it for you. I will be in Gainesville tomorrow. But it could be simply that your orbitals are not populated equally, than you obviuosly has lower symmetry than Oh. (...) Best wishes, Anatoli Korkin Anatoli Korkin Ph.D r40757@email.mot.com !!! New !!! Computational Chemist korkin@act.sps.mot.com still works, but change it to the new one !!! Tel: (602) 655-3171 Fax: (602) 655-2285 Predictive Engineering Lab Semiconductor Products Sector Arizona Technology Motorola Inc., MD M350 Laboratories 2200 West Broadway Road Mesa AZ 85202 --------------------------------------------------- Date: Sat, 22 Nov 1997 12:31:26 -0800 From: "Ananikov V.P." Subject: Re2: CCL:G:atomic symmetry in G94 Dear Georg, A few additional comments concerning your request on Fe+. The close question has been discussed in GAMESS-Users-List, and here is one of the messages: ____________________________________________________________________________ Subject: Re: GU: Symmetry of atoms Date: Mon, 17 Nov 1997 10:02:02 -0600 (CST) From: kurt@si.fi.ameslab.gov (Kurt Glaesemann) Reply-To: gamess-users@majordomo.umd.edu To: gamess-users@majordomo.umd.edu >When I want to perform some calculations on atoms (or monoatomic ions), I wonder about the symmetry to choose. There are 2 input examples dealing with atoms, and they both have the symmetry D2h. Is that a generally acceptable choice? If not, what should the choice be based upon? It's the higher albelian group. It will keep your x, y, and z pure. This of course, assumes that the electron density easily symetric. If you do Fe+, you have to choose group=c1 in $DRT and state average the sextet, so that all d's are equivelent, otherwise they are inequivelent. ____________________________________________________________________________ best regards, Valentin. Valentin P. Ananikov NMR Laboratory N.D. Zelinsky Institute of Organic Chemistry Leninsky Prospect 47 Moscow 117913, Russia e-mail: val@nmr1.ioc.ac.ru http://nmr1.ioc.ac.ru/Staff/AnanikovVP/ Fax (7095) 1355328 Phone (7095) 9383536, (7095) 1359094 --------------------------------------------------- Date: Mon, 24 Nov 1997 10:23:46 -0500 From: Brian Teppen Hi, Georg: I have done HF/DFT calculations on Fe complexes, and have naturally suffered convergence problems. One trick that seems to often work is to do an initial single-point calculation using STO-3G. Give it many cycles (say, MaxCycle=200) because they are cheap. Then, use the STO-3G wavefunction as the initial guess for some Gaussian basis set. It might be worth a try. Best wishes, Brian J. Teppen teppen@srel.edu Advanced Analytical Center for Environmental Sciences Savannah River Ecology Laboratory University of Georgia Drawer E Aiken, SC 29802 phone:803-725-8157 fax:803-725-3309 --------------------------------------------------- END OF SUMMARY -- Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ From gsfc@cts.com Thu Nov 27 18:37:47 1997 Received: from mh2.cts.com for gsfc@cts.com by www.ccl.net (8.8.3/950822.1) id SAA27161; Thu, 27 Nov 1997 18:32:39 -0500 (EST) Received: from king.cts.com (root@king.cts.com [198.68.168.21]) by mh2.cts.com (8.8.7/8.8.5) with ESMTP id PAA14437 for ; Thu, 27 Nov 1997 15:32:41 -0800 (PST) Received: from crash.cts.com (root@crash.cts.com [192.188.72.17]) by king.cts.com (8.8.7/8.8.7) with SMTP id PAA09550 for ; Thu, 27 Nov 1997 15:32:40 -0800 (PST) Received: from gsfc.cts.com by crash.cts.com with smtp (Smail3.1.29.1 #5) id m0xbDPM-00004sC; Thu, 27 Nov 97 15:31 PST Message-Id: Date: Thu, 27 Nov 97 15:31 PST X-Sender: gsfc@crash.cts.com (Unverified) X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Richard Essery & Grazyna Oszczygiel Subject: Need help English>Polish Hello from San Diego I need the Polish for the following substances. If you can help me I would really appreciate it. If not, please forward this request on to someone who may be able to help. Thanks, and if there is anything we can do for you here San Diego, please let us know. Rich and Grazyna ================================================ ethyl isopropyl ketone ethylenediaminetetraacetic acid sodium salt hydroquinone bis(2-hydroxyethyl) ether poly((dimethyl co-methyl-(6-diozo-5,6-dihydro-5-oxo-1-naphthylenesulphonylamino)propyl)silo xane) propylene glycol monomethyl ether acetate tert-butylamine borane 1,3-diamino-2-propanoltetraacetic acid tetrapotassium salt Richard Essery and Grazyna Oszczygiel Phones: 800-770-4729 and 619-275-2932 FAX: 619-275-1166 or 619-448-4387 Address: 1640 N. Johnson Ave. El Cajon, CA 92020 CompuServe: 103330.3722@compuserve.com Internet: gsfc@cts.com From yubofan@guomai.sh.cn Thu Nov 27 22:37:46 1997 Received: from guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id WAA27911; Thu, 27 Nov 1997 22:17:19 -0500 (EST) Received: from default (Email-42 [210.0.0.10]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id LAA15131 for ; Fri, 28 Nov 1997 11:11:27 +0800 (CST) Message-Id: <199711280311.LAA15131@guomai.sh.cn> From: "yubofan" To: Subject: Summary: CCL:Need some reference about molecular geometry optimization. Date: Fri, 28 Nov 1997 09:14:38 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1157 MIME-Version: 1.0 Content-Type: text/plain; charset=HZ-GB-2312 Content-Transfer-Encoding: 8bit Hi, I am doing geometry optimization of a big molecule. I think it is impossible for me to do these jobs for the whole molecule which contains over 40 C atoms, so I want to split it into several parts and calculate each of them respectively. Then I will put them together. Is this thought possible? If possible, could you please give me some advice or reference with the same kind of work. With best regards Y. Fan ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641470 Shanghai, 200433 P. R. China ============================================================= Hi Yubo, There's a method called "Divide-and Conquer" ( See: "A density-matrix divide-and-conquer approach for electronic structure of large molecules", Weitao Yang and Tai-Suang Lee, J.Chem.Phys., 103(13),5674,1995) may solve your problem. I know the method is not easy to use if you don't have programs in your hand, but at least the paper can supply some clues to help you thinking. Best wishes! Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92612 | \/ | Lao-tzu (604-531 B.C.)| +-----------------------+------------------+-------------------------+ Since you say it is impossible to optimize the geometry for the whole molecule, I assume you are using quantum mechanics (ab initio etc.) or semi- empirical methods. This would however be no problem with the use of molecular mechanics calculations which are supported by a lot of programs: AMBER, CHARMM, GROMOS, XPLOR, ChemX, Hyperchem etc. etc. Best regards, Eldbjoerg S. Heimstad dear yubo there is one dft program called the amsterdam density functional ADF 2.x where you can put together your molecule from fragments. These fragments itself are built with basic atoms, the smallest fragments possible. For more information see http://tc.chem.vu.nl./SCM/welcome.html. For organic molecules it is often absolute adequate to use semi-empirical methods like PM3 or MNDO to get qualitatively sufficient results. With these methods you can calculate even big molecules with more than 40 atoms. There was a intersting discussion going on last month about semi-empirical methods, look for the summary about extented hueckel methods initiated by E. Lewars CCL:EXTENDED HUECKEL--SUMMARY AND THANKS VERY MUCH CCL:EXTENDED HUECKEL--MORE INFO AND A FINAL SUMMARY I hope this information will help you christoph ---- Christoph Widauer Laboratorium f. Anorganische Chemie ETH-Zentrum CAB C8 Universit~{dt~}sstrasse 6 CH-8092 Zuerich Phone (Zurich): +41 (1) 632 61 19 Fax (Zurich): +41 (1) 632 10 90 e-mail: widauer@inorg.chem.ethz.ch Dear Mr. Fan, Have you tried some Molecular Mechanics calculation? It can select only the most promising structures, and then you could make your QM calculation just on them. Regards, -- ---------------------------------------------------------------------------- ------- Gustavo de Miranda Seabra MSc Student in Chemistry E-Mail: seabra@npd.ufpe.br Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil ---------------------------------------------------------------------------- ------- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641470 Shanghai, 200433 P. R. China ============================================================= From lavelle@mbi.ucla.edu Fri Nov 28 00:37:48 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id AAA28108; Fri, 28 Nov 1997 00:21:57 -0500 (EST) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by rho.ben2.ucla.edu (8.8.5/8.8.5) with SMTP id VAA26870; Thu, 27 Nov 1997 21:21:57 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA07346; Thu, 27 Nov 1997 21:21:57 -0800 Message-Id: <3.0.32.19971127212841.00a38500@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 27 Nov 1997 21:28:42 -0800 To: hyperchem@hyper.com, chemistry@www.ccl.net From: Laurence Lavelle Subject: Ab initio computational time. Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Hi all, Happy Thanksgiving to those in USA. I would very much appreciate any estimates (hrs) on the ab initio computational time of the following system: single point calculation, 731 basis functions, UHF, MP2, direct SCF Hardware: Dual pentium 200MHz, 256K external cache, 192MB RAM OS: Windows NT Workstation 4.0 SP3. Computational package: HyperChem 5.02 Although NT uses SMP, HyperChem is not a multithread application so the "computational system" is a single pentium 200MHz. I look forward to hearing from you. Laurence Lavelle
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From peter@cherwell.com Fri Nov 28 10:37:54 1997 Received: from congo.cherwell.com for peter@cherwell.com by www.ccl.net (8.8.3/950822.1) id KAA29980; Fri, 28 Nov 1997 10:35:51 -0500 (EST) Received: from mersey.cherwell.com ([193.82.249.217]) by congo.cherwell.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-0U10L2S100) with SMTP id AAA212 for ; Fri, 28 Nov 1997 15:35:32 +0000 Message-Id: <3.0.1.32.19971128153533.00865510@cherwell.com> X-Sender: peter@cherwell.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Fri, 28 Nov 1997 15:35:33 +0000 To: chemistry@www.ccl.net From: Peter Tebbutt Subject: Java Beans for Chemists Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers Beta Testers Required Cherwell Scientific Publishing are pleased to announce the latest development of the popular ChemSymphony software - ChemSymphony Beans. We are looking for beta-testers for our soon-to-be 'released', and by this message 'announced', suite: ChemSymphony Beans. ChemSymphony Beans is a collection of classes, images and additional resources for developing applications which use chemical structural information. The ChemSymphony Beans collection provides developers with a toolkit which will be especially useful in building corporate intranets linking databases, chemistry programs, and network resources. It will also be useful to chemistry software developers who wish to develop applications which build on the ChemSymphony architecture. All the components have an open interface which makes it easy to connect them to other JavaBeans components. ChemSymphony Beans should be of interest to anyone who wants to find out what JavaBeans can do for Chemistry. You are welcome to browse the draft documentation at: http://www.cherwell.com/CSBeans We wish to hear from any Java-experienced chemists who would be able to beta-test and report on these Beans in the next month. The Beans should be ready for beta-testing by December 5. We would like reports from testers by December 25. ChemSymphony Beans includes all the functionality to be found in the ChemSymphony suite on our www site. It also includes Beans for sketching 2D structures, for presenting multiple structures on the page (a Marquee panel), a cool tool (a Template Factory) for customising Marquees so as to incorporate heterogenous streams of data from database searches etc., new filters and explanations of how to write more filters and plenty more Beans. Best of all JavaBeans could be the promised land of software development: hooking these beans together is labor-saving, fun and easy! Please reply to peter@cherwell.com if you wish to be included in the beta-test program. Please mention any relevant experience that will help you to beta-test for us. I look forward to hearing from you. Peter Tebbutt --- --- Peter Tebbutt | e-mail: peter@cherwell.com Product Analyst | Tel: +44 (0)1865 784812 Cherwell Scientific Publishing | Fax: +44(0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.com --- --- --- Check Out ChemSymphony - - JARS Top 1% Web Applet --- --- http://www.chemsymphony.com - - http://www.jars.com --- --- --- From root@liposome.genebee.msu.su Sun Nov 30 13:38:23 1997 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id NAA07646; Sun, 30 Nov 1997 13:11:13 -0500 (EST) Received: from localhost (root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) with SMTP id VAA21822 for ; Sun, 30 Nov 1997 21:14:34 +0300 Date: Sun, 30 Nov 1997 21:14:33 +0300 (MSK) From: root To: chemistry Subject: a MD rookie's startup difficulties Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I've just recently started digging into this exciting field: computer modelling of large (bio)macromolecular system dynamics. Naturally, I am running into initial difficulties I am unable to resolve on my own. Since there are no MD wizards in my vicinity, I've decided to turn to the CCL list, which has in the past always been very helpful. Here's what I am trying to do: to study polycation-induced lateral segregation of lipid anions in lipid bilayers (actually, I'd like to do polycation-induced flip-flop, but that's pure SF just now) by means of molecular dynamics. (I can't dig Monte Carlo very well, and it seems to produce lots of artefacts, especially on lattices). Initially, I was thinking to start with the following system caricature: approximating the linear polycation by an linearly linked but otherwise unconstrained chain of Lennard-Jones balls, some of which are charged hovering in vacuum over an 2d array of LJ balls (some of them charged, either in a random distribution, or in contiguous blocks to mimick block copolymers) constrained in the z direction by a narrow parabolic potential well. Their movements are dampened in the xy plane. System's periodic boundary condition is suspended in the z direction. Both components are allowed to relaxate in isolation. The polycation should resemble a self-avoiding random walk with additional electrostatic repulsion. The same electrostatic repulsion should generate a roughly hexagonal ion pattern embedded into the neutral ball matrix. Alas, I soon realized existing packages offer no easy support for setting up such simple systems. Rolling one's own by modifying e.g. D.C. Rapaport's code form "The Art of Molecular Dynamics Simulation" was out of question due to lack of time. So I decided to skip this first step, progressing immediately to a physically realistic system which, paradoxically, seemed easier. While searching for free packages which, also, ran on Linux, I encountered VMD/NAMD, which seemed to offer the most advanced features. I found their advertised features as good scalability, capability to render publication-quality images, remote realtime visualization and realtime control of the running system (as introduction of perturbative forces) particularly appealing. Though so far I have been unable to compile NAMD under Linux and getting my binary tarball of VMD to work on my RedHat 4.2 Linux box, I got NAMD to work in single-node mode (built PVM, also, does not work quite right yet, but I'm working on it) under IRIX 5.3 on an SGI Indy. Another difficulty emerged: while I have been able to generate good *.pdb structures of polymers (so far only polyvinylpyrrolidone oligomers) with Gasteiger's CORINA email facility from manually constructed SMILES strings (is there an easier way?), I had no such luck with the according *.psf file. NAMD manual says they can be fashioned with XPLOR (which I do not have), or by hand. Since my system will get pretty large finally, I'd rather avoid the latter option. Is there another alternative I failed to notice? Since protein polycations tend to be rather stiff, and interesting effects start to occur only beyond the molecule segment's length, I'd rather avoid them. My ad hoc system of choice is a random vinylpyrrolidone/vinylamin copolymer. Does anybody study (nonrigid and/or solvated) polymeric polycations here? Finally, I'd like to inquire whether, and where, can one obtain simulation boxes with well-equilibrated hydrated lipid (bi/mono)layer patches, preferably with a fraction of the membrane lipids negatively charged. Thanks a lot, Eugene Leitl, MSU, Polymer Science Dept.