From chemistry-request@server.ccl.net Thu Mar 23 07:56:48 2000 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA25012 for ; Thu, 23 Mar 2000 07:56:47 -0500 From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 862568AB.00469351 ; Thu, 23 Mar 2000 06:50:52 -0600 X-Lotus-FromDomain: University of Nebraska@UNIVERSITY OF NEBRASKA To: chemistry@ccl.net Message-ID: <862568AB.00469176.00@unomail.unomaha.edu> Date: Thu, 23 Mar 2000 06:50:46 -0600 Subject: Cluster information and Linux Alpha Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CClers, If anyone could steer me in the right direction (or even give an answer :) ) with the following two queries (each containing several questions), I'd be most greatful. 1) Is it possible to combine Linux clusters over a LAN or by internet connection? Can an alpha Linux cluster be coupled with an Intel Linux cluster? Would the Linda distributed software package work in this cross-platform environment? 2) What is the status of a compiler for G98 under a Linux/alpha system. I queried Dr. Fox at Gaussian ca. 4 to 6 months ago about compiling Gaussian Linux/alpha and he stated that there was not a suitable compiler for Gaussian (using Linux/alpha) at that time. I know others on this list a have asked questions about compiling G98 on an Linux/alpha system with various problems. Is it possible? Does anyone know about the "Compaq" FORTRAN compiler for Linux/alpha and when it will be released? Anyone at the Portland group working on this? I'll stop here (and summarize my findings). Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 554-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Thu Mar 23 10:39:27 2000 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA25705 for ; Thu, 23 Mar 2000 10:39:27 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id RAA30330 for ; Thu, 23 Mar 2000 17:39:10 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Thu, 23 Mar 2000 17:39:09 +0200 (EET) From: Mikael Johansson X-Sender: mpjohans@soul.helsinki.fi To: chemistry@ccl.net Subject: HyperChem .hin to MOL2 converter (hin2mol2.py) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! I just finished a utility that converts a HyperChem .hin-file to a Tripos MOL2-file, keeping the charges. It's again written in Python, so you will need an interpreter. Use the program to whatever, I use it to make ligand files for AutoDock. ANOTHER NOTE! if you already got the v0.9 version of hin2pdbq, get the latest, v0.95! v0.9 contains a bug which makes the proggie ignore the first atom of every sub-molecule after the first one... Both programs can be obtained here: http://www.helsinki.fi/~mpjohans/python Comments, bug-reports etc. as always welcome. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi From chemistry-request@server.ccl.net Thu Mar 23 10:47:35 2000 Received: from mail.wesleyan.edu (smtp.wesleyan.edu [129.133.1.61]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA25787 for ; Thu, 23 Mar 2000 10:47:34 -0500 Received: from seahorse (seahorse.chem.wesleyan.edu [129.133.20.16]) by mail.wesleyan.edu (8.9.3/8.9.1) with ESMTP id KAA16148 for ; Thu, 23 Mar 2000 10:47:16 -0500 (EST) Message-Id: <4.2.0.58.20000323104829.00a58340@mail.wesleyan.edu> X-Sender: yliu@mail.wesleyan.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Thu, 23 Mar 2000 10:54:26 +0000 To: chemistry@ccl.net From: Yongxing Liu Subject: two state ising model Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCLers, I am looking for an old ref. paper by Dr. W. Kauzmann on water ( two state ising model) with no luck. I tried a lot of search methods with the following criteria : (1) It is published on J. Chim. Phys. ( french journal of J. Chem. Phys.) (2) Authored by Dr. W. Kauzmann (3) It's on water two state ising statistic model. I am wondering if somebody happens to know this reference(date). Thanks a lot in advance. Sincerely, ------------------------------------- Yongxing Liu Department of Chemistry Wesleyan University Middletown CT 06459 Tel: 860-685-2777 ------------------------------------- From chemistry-request@server.ccl.net Thu Mar 23 10:57:04 2000 Received: from eros.iqm.unicamp.br (eros.iqm.unicamp.br [143.106.51.200]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA25852 for ; Thu, 23 Mar 2000 10:56:47 -0500 Received: by eros.iqm.unicamp.br (Postfix, from userid 13555) id C4F213D43; Thu, 23 Mar 2000 12:56:15 -0300 (EST) Date: Thu, 23 Mar 2000 12:56:15 -0300 From: vazquez To: Tapas Kar Cc: Bernd Engels , Computational Chemistry List Subject: Re: CCL:electrostatic potential Message-ID: <20000323125615.A32586@eros.iqm.unicamp.br> References: <200003221237.NAA13933@rs5.thch.uni-bonn.de> <004601bf9410$3dc87c40$5363e683@thchem.siu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0.1i In-Reply-To: <004601bf9410$3dc87c40$5363e683@thchem.siu.edu>; from tapaskar@siu.edu on Wed, Mar 22, 2000 at 09:06:46AM -0600 Hello OpenDX can do the job very too (www.opendx.org) Pedro On Wed, Mar 22, 2000 at 09:06:46AM -0600, Tapas Kar wrote: > > Try Chem3D > ---------------------------------------------------- > Tapas Kar > ---------------------------------------------------- > From: Bernd Engels > Sent: Wednesday, March 22, 2000 9:05 AM > Subject: CCL:electrostatic potential > > > Dear All, > > Somebody from here want to plot the electrostatic potential which he > > computed with G98 (gaussian cube file). > > Which plot program is the best. > > Bernd Engels From chemistry-request@server.ccl.net Thu Mar 23 13:42:03 2000 Received: from kalypso.iqm.unicamp.br (kalypso.iqm.unicamp.br [143.106.51.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA26885 for ; Thu, 23 Mar 2000 13:41:59 -0500 Received: by kalypso.iqm.unicamp.br (V-MTA, from userid 105) id B25EE7268B; Thu, 23 Mar 2000 15:41:26 -0300 (EST) Date: Thu, 23 Mar 2000 15:41:26 -0300 From: Pedro A M Vazquez To: Tapas Kar , Bernd Engels , Computational Chemistry List Subject: Re: CCL:electrostatic potential Message-ID: <20000323154126.A41746@kalypso.iqm.unicamp.br> References: <200003221237.NAA13933@rs5.thch.uni-bonn.de> <004601bf9410$3dc87c40$5363e683@thchem.siu.edu> <20000323125615.A32586@eros.iqm.unicamp.br> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0pre4i In-Reply-To: <20000323125615.A32586@eros.iqm.unicamp.br>; from vazquez@eros.iqm.unicamp.br on Thu, Mar 23, 2000 at 12:56:15PM -0300 |o|... Thu, Mar 23, 2000 at 12:56:15PM -0300, vazquez ...|o| wrote: > Hello > OpenDX can do the job very too (www.opendx.org) Oops, I mean `very well too' , I've put a small example of an OpenDX network at http://kalypso.iqm.unicamp.br/pot/pot.tar.gz it has the following relevant files: cube.dx the cube data in dx format cube.net the dx network water.com the g94 input file water.cube the output cube water.dx the water molecule dx input file water.log the g94 output file I hope this helps Pedro From chemistry-request@server.ccl.net Wed Mar 22 22:41:26 2000 Received: from yakko.cimav.edu.mx (root@[207.248.161.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA22191 for ; Wed, 22 Mar 2000 22:41:25 -0500 Received: from glossman ([207.248.161.148]) by yakko.cimav.edu.mx (8.9.3/8.9.3) with SMTP id UAA29615 for ; Wed, 22 Mar 2000 20:47:52 -0700 Message-ID: <001801bf9482$1273c6e0$94a1f8cf@cimav.edu.mx> From: "Dr. Daniel Glossman" To: "Computational Chemistry List" Subject: NLO properties Date: Wed, 22 Mar 2000 20:41:34 -0800 Dear netters: Which programs (commercial or not) are available for the calculation of the non linear optical properties of molecules, materials and/or polymers? (for the Windows environment). Thanks in advance Dr. Daniel Glossman Mitnik ************************************************************************* Dr. Daniel Glossman Mitnik Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) Departamento de Pol=EDmeros = Phone: (52) 1 4391151 Miguel de Cervantes 120 = FAX: (52) 1 4391112 Complejo Industrial Chihuahua = E-mail: glossman@mail.cimav.edu.mx Chihuahua, Chih. 31109 = glossman@hotmail.com Mexico *************************************************************************= From chemistry-request@server.ccl.net Thu Mar 23 05:56:40 2000 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA23762 for ; Thu, 23 Mar 2000 05:56:32 -0500 Received: by lgdx04.lg.ehu.es id AA08635; Thu, 23 Mar 2000 11:55:32 +0100 Message-Id: <200003231055.AA08635@lgdx04.lg.ehu.es> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Thu, 23 Mar 2000 12:00:05 +0100 Subject: Re: CCL:electrostatic potential From: "Pablo Vitoria" To: Bernd Engels , Computational Chemistry List Mime-Version: 1.0 X-Priority: 3 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA23763 Hi, Molden, a freeware and constantly updated program that I have been using for a while now (http://www.cmbi.kun.nl/~schaft/molden/molden.html), can display Gaussian cubes, print them as Postscript (very nice plots!), and even export them to POVRay, which produces high quality graphics. gOpenMol (http://www.csc.fi/~laaksone/gopenmol/gopenmol.html) can do it also, and you can even map the electrostac potential ont the density or any other surface (two cubes: density and EP). The program comes with utilities to transform Gaussian cubes to its own format. Best regards Pablo ----------------------------------------- Pablo Vitoria Garcia Dpto. Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Aptdo. 644 E-48080 Spain Phone: +34 94 6012000 Ext. 5529 Fax: +34 94 4648500 ----------------------------------------- ---------- >From: Bernd Engels >To: chemistry@server.ccl.net (Computational Chemistry List) >Subject: CCL:electrostatic potential >Date: juev., 11 mayo 1939 13:37 > > Dear All, > > Somebody from here want to plot the electrostatic potential which he computed > with G98 (gaussian cube file). > > Which plot program is the best. > > Bernd Engels > Inst. f¸r Org. Chemie > Universit”t W¸rzburg > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Thu Mar 23 11:07:39 2000 Received: from si.fi.ameslab.gov (si.fi.ameslab.gov [147.155.20.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA25952 for ; Thu, 23 Mar 2000 11:07:39 -0500 Received: (from pradipta@localhost) by si.fi.ameslab.gov (AIX4.2/UCB 8.7/8.7) id KAA18928 for chemistry@ccl.net; Thu, 23 Mar 2000 10:07:32 -0600 (CST) From: Pradipta Bandyopadhyay Message-Id: <200003231607.KAA18928@si.fi.ameslab.gov> Subject: Mistake in the IPCM question! To: chemistry@ccl.net (CCL) Date: Thu, 23 Mar 2000 10:07:32 -0600 (CST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text hi everyone, I had a mistake in my question about IPCM model. I wrote ___________________________________________ Hi everyone, What is value of the density used in the isodensity surface construction in the IPCM model ( I mean what is the default value in GAUSSIAN 94)? Also the unit of the solute(*) cavity in the IPCM model - is it Angstrom3 (cube)?. Thanks. Pradipta -------__________________________________________ I want to know the unit of the VOLUME of the solute cavity - I forgot to add VOLUME in the last mail. Thanks. Pradipta -- ***************************************** * Dr. Pradipta Bandyopadhyay * * AMES LAB * * Department of Chemistry * * Iowa State Unievrsity * * Ames, IA 50011 * * USA * * e-mail: pradipta@si.fi.ameslab.gov * * Phone : 515-294-4604 (Lab) * * : 515-232-8067 (Residence) * * Fax : 515-294-0105 * * URL: http://www.msg.ameslab.gov/ * * Group/pradipta/index.html * ***************************************** ------------------------------------------------------------------------------ You may my glories and my state dispose, But not my griefs; still am I king of those. -- William Shakespeare, "Richard II" ------------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Mar 23 12:24:35 2000 Received: from oulu.fi (root@ousrvr.oulu.fi [130.231.240.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA26553 for ; Thu, 23 Mar 2000 12:24:29 -0500 Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by oulu.fi (8.8.5/8.8.5) with ESMTP id TAA07739 for ; Thu, 23 Mar 2000 19:24:15 +0200 (EET) Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by paju.oulu.fi (8.8.5/8.8.5) with ESMTP id TAA19024510 for ; Thu, 23 Mar 2000 19:24:14 +0200 (EET) Date: Thu, 23 Mar 2000 19:24:14 +0200 From: Atte Sillanpaa X-Sender: asillanp@paju.oulu.fi To: chemistry@ccl.net Subject: Summary of activation free energy In-Reply-To: <862568AB.00469176.00@unomail.unomaha.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII First of all thanks for everyone who replied. From the responses I gather that searching for a free energy maximum based on potential energy surface even if there is no extremum on the PES is a sound approach. The program POLYRATE, which Jordi suggested, gives possibility to use more sophisticated theories to calculate rate constants. As another alternative Cory Pye suggested the thermodynamic integration scheme from constrained molecular dynamics. The responses (slightly edited to save space) were: --------8<------------------------- From: Cory Pye On Wed, 15 Mar 2000, Atte Sillanpaa wrote: > Hello CCLers, > I'm trying to calculate the free energy of activation for a process where > there is no minimum on the potential energy surface (PES). The (ethene > polymerisation termination) reaction begins with > a beta elimination from an alkyl group to the metal center. This forms a > fairly unstable metal hydride and a hapto2-alkene. The PES for scanning > the alkene away from the metal increases monotonically approaching the > separated products value. The free energy of separated products is readily > calculated, and is naturally much lower relative to PE. However, as the > alkene recedes from the metal it gradually gains the translational and > rotational degrees of freedom and its free energy drops, but there is a > maximum at some point. > > The question is that if I calculate the free energy with the harmonic > approximation at some (ambigious) constrained geometry (distance from the > metal) is it of any approximate value for the free energy of activation? If you use this approach, you would probably have to select some "reaction coordinate" and calculate the free energy at some selected points along your coordinate, say every 0.5 angstroms, to roughly locate your Free energy transition structure. Then you could refine the region near the maximum. > > Is there some other method for calculating the free energy of activation > in this kind of PES? > Another way is to calculate the free energy using constrained molecular dynamics with a DFT energy. Tom Ziegler's group at the U of Calgary has done these types of simulations (I was a post-doc there with him on a different project). Check out: 1) JACS 118 4434-4441 (1996) - Cp2Zr(C2H5)+ + C2H4 2) JACS 118 13021-13030 (1996) - (CpSiH2NH)TiR+ + C2H4 I. 3) Organometallics 16 3454-3468 (1997) - "" II. 4) JACS 119 6177-6186 (1997) - Ni(II)-diimine + C2H4 5) JPC B 101 7877-7880 (1997) - NI(II)-diimine + C2H4 6) JACS 120 2174-2175 (1998) - Ti(IV)-H2 7) "Transition State Modelling for Catalysis", D. G. Truhlar and K. Morokuma, (eds), ACS Symp. Ser. 721, ACS, Washington, D.C. (1999), p173-186 8) Catalysis Today 50 479-500 (1999) - overview ************* ! Dr. Cory C. Pye ***************** ! Assistant Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye@crux.stmarys.ca http://husky1.stmarys.ca/cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) ----8<----------------------- From: Jordi =?iso-8859-1?Q?Vill=E0?= Dear Atte, take a look at GAUSSRATE (http://comp.chem.umn.edu/sds/), which you can use for calculating the free energy profile for your reaction using Variational Transition State Theory (VTST), even if you don't have any maximum on the PES. In principal you have two general approaches to use for solving your problem using VTST. The first is the use of the geometries generated by an intrinsic reaction path (IRC) calculation and the second is using a simple distinguished reaction coordinate (DCP). Both of these possibilities can be readily explored using GAUSSRATE (for automatically calculate the needed structures if you have Gaussian installed in your computer) or its father POLYRATE (if you have previously calculated those paths and you kept first and second derivatives along them) Jordi -- Jordi Villa i Freixa Department of Chemistry, University of Southern California 3620 S McClintock Av. #418; Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 jorgevil@usc.edu http://laetro.usc.edu/jorgevil ----------8<----------------------- From: michael braunschweig hi atte, to obtain an trasition state try to calculate a first order saddle point on the pes without making any constrains. to find the start structure make a quadratic synconous transit. to be sure this is a valid transition state make a frequency calculation (one imaginary frequency) and compute an irc-run. in g98 the keywords are: opt=qst2 (or qst3), opt=ts and irc. hope this will help michael braunschweig university of dortmund department of chemistry germany atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 Oulun Yliopisto FINLAND | Entropy requires no maintenance. | From chemistry-request@server.ccl.net Thu Mar 23 13:54:52 2000 Received: from jmlopez.fam.cie.uva.es (aguado@jmlopez.fam.cie.uva.es [157.88.38.56]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA26968 for ; Thu, 23 Mar 2000 13:53:52 -0500 Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.9.1/8.9.1) id EAA16838 for chemistry@ccl.net; Wed, 22 Mar 2000 04:10:46 +0100 Date: Wed, 22 Mar 2000 04:10:46 +0100 From: Andres Aguado Message-Id: <200003220310.EAA16838@jmlopez.fam.cie.uva.es> To: chemistry@ccl.net Subject: CaO versus MgO... Dear All, I have found a lot of studies about several properties of MgO surfaces. Similar work on CaO surfaces seems to me to be scarce. Is there any special reason why MgO surface physics should be much more interesting than CaO (or other similar oxides) surfaces? Put it in another way, does anyone of you know if there are important differences between the surface properties of the alkaline earth oxides? Thanks a lot in advance, and best regards from Spain! Andres Aguado.