From chemistry-request@server.ccl.net Mon Nov 15 00:03:40 1999 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA20213 for ; Mon, 15 Nov 1999 00:03:39 -0500 Received: from voxopm.csc.fi (voxopm.csc.fi [128.214.248.23]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id GAA23669 for ; Mon, 15 Nov 1999 06:54:52 +0200 Date: Mon, 15 Nov 1999 06:54:52 +0200 From: Maija Lahtela To: chemistry@ccl.net Subject: Volume keyword in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I would like to ask about Volume-keyword. I am interested about the volume of molecule. But for example with following six input files I get different molar volumes: 1) Mem=150MW #p rhf/3-21g* Density=Current scf=tight volume test Box volume = 982.544 fraction occupied=0.116 Integrated density= 5.0945197336220325D+00 error=-4.9054802663779675D+00 Molar volume = 114.134 bohr**3/mol ( 10.185 cm**3/mol) Recommended a0 for SCRF calculation = 2.25 angstrom ( 4.26 bohr) 2) #p rhf/3-21g* Density=Current scf=tight volume test Box volume = 982.544 fraction occupied=0.141 Integrated density= 7.8469300328767240D+00 error=-2.1530699671232760D+00 Molar volume = 138.946 bohr**3/mol ( 12.399 cm**3/mol) Recommended a0 for SCRF calculation = 2.37 angstrom ( 4.48 bohr) 3) #p rhf/3-21g* scf=tight volume test Box volume = 982.544 fraction occupied=0.162 Integrated density= 8.7064056753546222D+00 error=-1.2935943246453778D+00 Molar volume = 158.795 bohr**3/mol ( 14.171 cm**3/mol) Recommended a0 for SCRF calculation = 2.46 angstrom ( 4.64 bohr) 4) %Mem=100MW #p rhf/3-21g* scf=tight volume test Box volume = 982.544 fraction occupied=0.152 Integrated density= 2.7978807764929656D+00 error=-7.2021192235070348D+00 Molar volume = 148.870 bohr**3/mol ( 13.285 cm**3/mol) Recommended a0 for SCRF calculation = 2.41 angstrom ( 4.56 bohr) 5) #p rhf/3-21g* opt scf=tight volume test Box volume = 982.544 fraction occupied=0.146 Integrated density= 7.0641561577918202D+00 error=-2.9358438422081798D+00 Molar volume = 143.908 bohr**3/mol ( 12.842 cm**3/mol) Recommended a0 for SCRF calculation = 2.39 angstrom ( 4.52 bohr) 6) %Mem=100MW #p rhf/3-21g* opt scf=tight volume test Box volume = 982.544 fraction occupied=0.126 Integrated density= 8.0829021488536519D+00 error=-1.9170978511463481D+00 Molar volume = 124.059 bohr**3/mol ( 11.071 cm**3/mol) Recommended a0 for SCRF calculation = 2.30 angstrom ( 4.35 bohr) How I should use Volume keyword to get the right volume of molecule ? Thanks in advance! Yours, Maija Lahtela-Kakkonen *************************************** Maija Lahtela-Kakkonen Researcher CSC-Center for Scientific Computing Tekniikantie 15 a D P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 FAX 358-9-4572302 E-MAIL mlahtela@csc.fi *************************************** From chemistry-request@server.ccl.net Sat Nov 13 22:54:11 1999 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA13777 for ; Sat, 13 Nov 1999 22:52:18 -0500 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id JAA10473 for ; Sun, 14 Nov 1999 09:12:16 +0530 Received: (from gadre@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id JAA04852 for CHEMISTRY@www.ccl.net; Sun, 14 Nov 1999 09:33:41 +0530 Date: Sun, 14 Nov 1999 09:33:41 +0530 From: "Prof. Shridhar R. Gadre" Message-Id: <199911140403.JAA04852@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: Alumni of Pune University Chemistry Dept. Dear Sirs/Madams: We, at the Department of Chemistry, University of Pune, are trying to make a complete database of our alumni. Pl. send me your e-mail address if you happen to be our alumnus. Thanks..............................Professor Shridhar Gadre From chemistry-request@server.ccl.net Sun Nov 14 18:04:13 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA18804 for ; Sun, 14 Nov 1999 18:04:13 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id RAA26780; Sun, 14 Nov 1999 17:55:40 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <382F3F0A.93CBCA93@syr.edu> Date: Sun, 14 Nov 1999 18:00:26 -0500 From: Deepak Singh Organization: Dept. of Chemistry, Syracuse University To: vmd-l@ks.uiuc.edu CC: Computational Chemistry List Subject: VMD question: changing font/color vmd labels? I posted this question on the vmd list a few days back, but did not get a reply. Here it is again: How does one change the font size/color on labels in vmd. I was unable to find any options in the menu. regards Deepak -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Mon Nov 15 03:36:15 1999 Received: from uvaix7e1.comp.UVic.CA (root@uvaix7e1.comp.UVic.CA [142.104.5.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA21187 for ; Mon, 15 Nov 1999 03:36:14 -0500 Received: from p17-31.dialup.UVic.CA (p17-31.dialup.UVic.CA [142.104.17.31]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id AAA128752 for ; Mon, 15 Nov 1999 00:27:38 -0800 From: royj@uvic.ca (Roy Jensen) To: CHEMISTRY@ccl.net Subject: Ionization of a molecule... Date: Mon, 15 Nov 1999 08:27:42 GMT Message-ID: <382fc057.28407258@pop.uvic.ca> X-Mailer: Forte Agent 1.5/32.451 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA21188 Is there a software package that will calculate the potential experienced by an electron as the parent molecule is ionized? I.e., calculate the energy as an electron is stepped further from the molecule (which is fixed in the optimized geometry). I am interested in determining the barrier as a polyanion is ionized. There is initially an attractive force holding the electron near the molecule. As the distance between the molecule (anion) and electron is increased, the dominant force becomes coulomb repulsion. Any references to published work would be appreciated. Roy Jensen From chemistry-request@server.ccl.net Mon Nov 15 05:36:19 1999 Received: from dogo.bq.ub.es (dogo.bq.ub.es [161.116.154.57]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21777 for ; Mon, 15 Nov 1999 05:36:06 -0500 Received: from dogo.bq.ub.es (localhost [127.0.0.1]) by dogo.bq.ub.es (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA58841 for ; Mon, 15 Nov 1999 11:25:49 -0800 (PST) Sender: bego@dogo.bq.ub.es Message-ID: <38305E3D.373C7F4A@dogo.bq.ub.es> Date: Mon, 15 Nov 1999 11:25:49 -0800 From: Bego Hernandez Organization: Universitat de Barcelona X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: multiple time step MD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL readers, Can someone send me references of multiple time step Molecular Dynamics? Thank you, Bego From chemistry-request@server.ccl.net Mon Nov 15 06:29:35 1999 Received: from tomir.uib.es (tomir.uib.es [130.206.33.91]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA22021 for ; Mon, 15 Nov 1999 06:29:29 -0500 Received: from ps.uib.es ([130.206.78.219]) by clust.uib.es (PMDF V5.2-32 #30169) with ESMTP id <01JID72PYLI68WW2LT@clust.uib.es> for chemistry@ccl.net; Mon, 15 Nov 1999 12:21:09 MET Date: Mon, 15 Nov 1999 12:24:50 +0100 From: miquel coll parets Subject: Summary: ZPE in DFT calculations To: chemistry@ccl.net Message-id: <382FED82.FBBE3B34@ps.uib.es> Organization: U.I.B. MIME-version: 1.0 X-Mailer: Mozilla 4.5 [ca]C- Softcatala (Win98; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: ca Hi evreyone, Three weeks ago, I posted the following question: I need some references about scaling factors of ZPE correction in DFT calculations (B3LYP/6-31+G*). Could anyone send me some information about this?. I appreciate very much the answers I got from Javier Ramos, E. Lewars and Qadir K. Timerghazin. Thank you all very much. Here are the list of references: C.W. Bauschlicher, Jr and H. Partridge J. Chem. Phys. 103, 1788 (1995) M.W. Wong Chem. Phys. Lett. (1996) A.P. Scott and L. Radom, Phys. Chem. 100, 16502 (1996) Best wishes Miquel Coll Dept. de Quimica, U.I.B. From chemistry-request@server.ccl.net Mon Nov 15 06:42:22 1999 Received: from idun.phc.chalmers.se (idun.phc.chalmers.se [129.16.97.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA22109 for ; Mon, 15 Nov 1999 06:42:21 -0500 Received: from andvare.phc.chalmers.se (andvare.phc.chalmers.se [129.16.97.75]) by idun.phc.chalmers.se (8.8.8/8.8.7) with ESMTP id MAA19154; Mon, 15 Nov 1999 12:33:44 +0100 Received: (from svedung@localhost) by andvare.phc.chalmers.se (8.8.8/8.8.8) id MAA16088; Mon, 15 Nov 1999 12:33:42 +0100 (MET) Date: Mon, 15 Nov 1999 12:33:40 +0100 (MET) From: Harald Svedung To: Bego Hernandez cc: chemistry@ccl.net Subject: Re: CCL:multiple time step MD In-Reply-To: <38305E3D.373C7F4A@dogo.bq.ub.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I usually use the Gauss-Radau variable time step integrator: E. Everhart, in: A.Carusi, G. B. Valsecchi (Eds.) Dynamics of Comets: Their Origin and Evolution, Reidel, Dordrecht, 1985, p. 185. For an evaluation of this method in the context of molecular dynamics se: K. Bolton, S. Nordholm, J. Comp. Phys. 113 (1994) 320. I can say, It does conserve energy! :-) /Harald On Mon, 15 Nov 1999, Bego Hernandez wrote: > Dear CCL readers, > > Can someone send me references of multiple time step Molecular Dynamics? > > > Thank you, Bego > > -= 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 > > > > > Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Mon Nov 15 09:51:39 1999 Received: from prserv.net (out1.prserv.net [165.87.194.252]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA23735 for ; Mon, 15 Nov 1999 09:51:38 -0500 From: jmmckel@attglobal.net Received: from schutz ([32.100.233.126]) by prserv.net (out1) with SMTP id <1999111514425925203gkeeue>; Mon, 15 Nov 1999 14:43:00 +0000 Message-ID: <38312982.4FAF@attglobal.net> Date: Tue, 16 Nov 1999 09:53:06 +0000 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: Bernd Melchers CC: Benny Moritz , chemistry@ccl.net Subject: Re: CCL:Chkpt File References: <3.0.6.32.19991111162611.009257e0@chem.boisestate.edu> <382C8CA8.46F4DBBA@fu-berlin.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Bernd Melchers wrote: > > Benny Moritz wrote: > > > Dear Netters, > > > > How do I read a checkpoint file? I have been unable to read my checkpoint > > files in GaussView (G98). I have been using an FTP program (CuteFTP) and > > all my gaussian jobs are stored in one directory, so I decided to make > > sub-directories to sort out all my jobs. I transferred the files from the > > FTP to my personal computer and then back into their appropriate > > sub-directories using ASCII mode for both transfers. But when I go into > > GaussView to view my checkpoint file an error message comes up saying > > unable to read checkpoint file. Is there anyway to fix my problem, or am I > > screwed? > > why the h*ll did you transfer the binary checkpoint file in ascii mode? It seems, > you are alone. There is no way back! > > Ciao > Bernd > > -= 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 I propose patience and temperance in answers sent to CCL... We are all uninformed at some level. John McKelvey From chemistry-request@server.ccl.net Mon Nov 15 10:25:30 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA23901 for ; Mon, 15 Nov 1999 10:25:30 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id JAA28499; Mon, 15 Nov 1999 09:16:51 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.1b+Sun/8.9.1) id JAA10791; Mon, 15 Nov 1999 09:16:50 -0600 (CST) From: John Stone Message-Id: <199911151516.JAA10791@geneseo.ks.uiuc.edu> Subject: Re: question To: desingh@syr.edu (Deepak Singh) Date: Mon, 15 Nov 1999 09:16:50 -0600 (CST) Cc: vmd-l@ks.uiuc.edu, chemistry@ccl.net In-Reply-To: <382F3F0A.93CBCA93@syr.edu> from Deepak Singh at "Nov 14, 99 06:00:26 pm" X-Mailer: ELM [version 2.4ME+ PL15 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > I posted this question on the vmd list a few days back, but did not get > a reply. Here it is again: > > How does one change the font size/color on labels in vmd. I was unable > to find any options in the menu. Presently there is no way to alter either one, although we are planning on changing this. We will likely add new VMD Tcl commands to alter the properties of label (and other) text. John Stone vmd@ks.uiuc.edu -- Theoretical Biophysics Group Email: johns@ks.uiuc.edu Beckman Institute http://www.ks.uiuc.edu/~johns/ University of Illinois Phone: (217) 244-3349 405 N. Mathews Ave FAX: (217) 244-6078 Urbana, IL 61801, USA Unix Is Good For You!!! From chemistry-request@server.ccl.net Mon Nov 15 05:06:35 1999 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21646 for ; Mon, 15 Nov 1999 05:06:35 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with SMTP id EAA28065; Mon, 15 Nov 1999 04:57:58 -0500 (EST) Date: Mon, 15 Nov 1999 04:57:58 -0500 (EST) From: "C.F. Matta" To: Roy Jensen cc: CHEMISTRY@ccl.net Subject: Re: CCL:Ionization of a molecule... In-Reply-To: <382fc057.28407258@pop.uvic.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Roy, With reference to your question: > Is there a software package that will calculate the potential > experienced by an electron as the parent molecule is ionized? I.e., > calculate the energy as an electron is stepped further from the > molecule (which is fixed in the optimized geometry). If I understand you correctly, you need something like the potential-energy profile of say a diatomic molecule A-B as you stretch the A-B separation, except that in your case B is an electron. This sort of question is OK when A and B are atoms, i.e. entities sufficiently massive to behave classically. However when B is an electron, the question looses all meaning since the electron (B) can no longer be localized to a sequence of points, as it flys away from the molecule. This is a direct consequence of the Heizenberg's uncertainity principle. I hope this helps, but I think your question is interesting. Take care. Cherif ....................................................................... Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ....................................................................... From chemistry-request@server.ccl.net Mon Nov 15 05:51:52 1999 Received: from email.guomai.sh.cn (cxxcnhgnvp@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21888 for ; Mon, 15 Nov 1999 05:50:48 -0500 Received: from guomai.sh.cn ([202.101.13.60]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with ESMTP id <0FL80096EJ1NU0@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Mon, 15 Nov 1999 18:41:48 +0800 (CST) Date: Mon, 15 Nov 1999 18:44:35 +0800 From: Yubo Fan Subject: Two options in SCRF calculation of G98 To: CHEMISTRY@ccl.net Message-id: <382FE413.A708260D@guomai.sh.cn> Organization: Fudan University MIME-version: 1.0 X-Mailer: Mozilla 4.6 [en] (Win98; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, I am doing some G98W calculation including solvent effects. When I used the keyword SCRF, I found two new dipole model options(A0=val and Dielectric=val). I read the manual carefully and I still don't understand how to use them. For example, if dimethyl sulfide molecule is wanted to be optimized on the level of B3LYP/6-31G* in dimethyl sulfide solution (A0=3.64 angstrom, Dielectric=6.2), how should I write the route section line? Please give me the detail line. Thank you very much. Sincerely yours Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Mon Nov 15 12:07:17 1999 Received: from imo16.mx.aol.com (imo16.mx.aol.com [198.81.17.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA24375 for ; Mon, 15 Nov 1999 12:07:17 -0500 From: AMUCS@aol.com Received: from AMUCS@aol.com by imo16.mx.aol.com (mail_out_v24.4.) id g.0.abbde108 (4319) for ; Mon, 15 Nov 1999 11:56:30 -0500 (EST) Message-ID: <0.abbde108.2561953e@aol.com> Date: Mon, 15 Nov 1999 11:56:30 EST Subject: GALAXY Version 2.7--- AlogP based Atom Type for Predicting Drug-Like Molecules To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Windows AOL sub 45 GALAXY Version 2.7 Release - AlogP based Atom Type Classification for Predicting Drug-Like Molecules. AM Technologies Inc., is pleased to announce the release of GALAXY Version 2.7 for all purpose molecular modeling and drug design software package. This software is extremely powerful for developing methods for predicting DRUG-LIKE molecules and physicochemical properties using authentic AlogP atom type and related tools. It is equally good for performing most advanced protein-ligand simulation, 3D-QSAR and molecular database analysis. Please visit our web page http://www.am-tech.com/ for further details. Please send inquiries to info@am-tech.com for further information. Thank you for your cooperation. From chemistry-request@server.ccl.net Mon Nov 15 12:45:25 1999 Received: from pegasus.physik.unizh.ch.physik.unizh.ch (pegasus.physik.unizh.ch [130.60.164.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA24538 for ; Mon, 15 Nov 1999 12:45:25 -0500 Received: [from physik.unizh.ch (pliberse@xcap4.physik.unizh.ch [130.60.164.30]) by pegasus.physik.unizh.ch.physik.unizh.ch (8.8.8/) with ESMTP id RAA03454 for ; Mon, 15 Nov 1999 17:36:43 GMT] Sender: pliberse@physik.unizh.ch Message-ID: <383044B1.C49823FE@physik.unizh.ch> Date: Mon, 15 Nov 1999 18:36:49 +0100 From: Samo Plibersek X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.9 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:ECP:Mn Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, Does anyone know where to find the effective core potential for Mn, with 22 core electrons replaced by the pseudopotential. I have already tried at EMSL server and in database of Institut für Theoretische Chemie, Universität Stuttgart. Thanks in advance, Samo Plibersek ----------------------------------------------------------------- Samo Plibersek Physik Institut der Universitaet Zuerich Winterthurerstrasse 190, 8057 Zuerich Switzerland pliberse@physik.unizh.ch 0041-1-6354585 From chemistry-request@server.ccl.net Mon Nov 15 13:36:37 1999 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA25068 for ; Mon, 15 Nov 1999 13:36:37 -0500 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id KAA04428 for chemistry@ccl.net; Mon, 15 Nov 1999 10:27:57 -0800 From: Schrodinger Info account Message-Id: <199911151827.KAA04428@canter-n-siegel.schrodinger.com> Subject: TITAN Introductory Workshop To: chemistry@ccl.net Date: Mon, 15 Nov 1999 10:27:56 -0800 (PST) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Wavefunction and Schrodinger formally invite you to a free, one-day molecular modeling seminar and hands-on workshop using Titan software. This workshop attempts to bring experimental scientists to the computational frontier in order to introduce the application of molecular modeling into daily research. The workshop will run from 10:00 AM until 3:00 PM and will include morning lectures by W.J. Hehre, lunch, and an afternoon "hands-on" tour of Titan including use of the Cambridge Structural Database. DATES and LOCATIONS: Thursday, December 2, Houston Monday, December 13, Philadelphia Tuesday, December 14, Chicago For more information, or to register, please visit http://www.schrodinger.com/Forms/titan_workshop.html. If you have any questions or comments, please contact either Jim Parisi at Wavefunction [email: jim@wavefun.com, phone: +1 949 955-2120], or Dr. Shi-Yi Liu at Schrodinger [email: syl@schrodinger.com, phone: +1 503 299-1150]. From chemistry-request@server.ccl.net Mon Nov 15 15:38:06 1999 Received: from chthry.chem.lsu.edu (root@chthry.chem.lsu.edu [130.39.128.124]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA25689 for ; Mon, 15 Nov 1999 15:38:06 -0500 Received: from localhost (charwel@localhost) by chthry.chem.lsu.edu (8.9.3/8.9.3) with ESMTP id OAA16327 for ; Mon, 15 Nov 1999 14:29:23 -0600 Date: Mon, 15 Nov 1999 14:29:22 -0600 (CST) From: Chris To: ccl Subject: acs-like bibtex style sheet? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hello, i am still discovering the joys of latex and bibtek. i am wondering if anyone has a bibtex style for an american chemical society journal, i.e. journal of physical chemistry? if you have such a style sheet, could you please send it to me? thanks, chris charwel@chthry.chem.lsu.edu From chemistry-request@server.ccl.net Mon Nov 15 15:42:05 1999 Received: from mailserv.molienergy.bc.ca (fireserv.molienergy.bc.ca [207.216.249.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA25739 for ; Mon, 15 Nov 1999 15:42:03 -0500 Received: by mailserv.molienergy.bc.ca with Internet Mail Service (5.5.2448.0) id ; Mon, 15 Nov 1999 12:32:02 -0800 Message-ID: <71B30885B657D111809D080009EEBBF3BB1051@mailserv.molienergy.bc.ca> From: Jan Reimers To: "'kynn@panix.com'" Cc: "'CHEMISTRY@ccl.net'" , "'amf@arches.uga.edu'" Subject: RE: [Q] Multiple histogram method Date: Mon, 15 Nov 1999 12:32:00 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain One thing that helps is to further average over all possible origins in time (t_o) as follows I think it is also better to use the differential form: Average over t_o {(-^2)/(-^2)} = exp(-t/tau) solve for tau for various small values of t. Once t gets large the average will fluctuate around zero and you cannot use these numbers. I have copied Alan Ferrenberg in case he wants to add anything. Hope this helps. JR > ---------- > From: kynn@panix.com[SMTP:kynn@panix.com] > Sent: Friday, November 12, 1999 5:35 PM > To: CHEMISTRY@ccl.net > Subject: CCL:[Q] Multiple histogram method > > > > > > > Several works (e.g. [1, 2]) reporting multiple histogram techniques to > construct a free-energy surface, use a formulas containing a factor g, > which equals (1 + 2*tau), where \tau is referred to as the "integrated > correlation time". The exact definition of tau is given in pp. 33-34 > of [3], and amounts to the integral with respect to t from 0 to > infinity of - ^2 divided by the variance of A, where A > is some quantity of interest. I have tried to obtain numerically the > tau used in the multiple histogram techniques, but no matter how much > data I amass, I still end up with something that doesn't come even > close to converging (i.e. the integral above fluctuates widely > throughout as one lets the upper limit of integration grow to > infinity). > > Does anybody know where I can find more info on how to compute this tau? > > Thanks! > > KJ > > [1] Ferrenberg, A. M. and Swendsen, R. H. "Optimized Monte Carlo Data > Analysis", 1989, Phys. Rev. Lett. 63(12) 1195-1198. > > [2] Kumar, S., et al. "The Weighted Histogram Analysis Method for > Free-Energy Calculations on Biomolecules. I. The Method", 1992, > J. Comp. Chem., 13(8) 1011-1021. > > [3] Binder, K. and Heermann, D. W. "Monte Carlo Simulation in > Statistical Physics", 2nd Corr. Ed., 1992, pp. 33-34. > > -= 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 Mon Nov 15 16:24:47 1999 Received: from mailserv.molienergy.bc.ca (fireserv.molienergy.bc.ca [207.216.249.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA25961 for ; Mon, 15 Nov 1999 16:24:40 -0500 Received: by mailserv.molienergy.bc.ca with Internet Mail Service (5.5.2448.0) id ; Mon, 15 Nov 1999 13:14:54 -0800 Message-ID: <71B30885B657D111809D080009EEBBF3BB1053@mailserv.molienergy.bc.ca> From: Jan Reimers To: "'kynn@panix.com'" Cc: "'CHEMISTRY@ccl.net'" , "'amf@arches.uga.edu'" Subject: RE: [Q] Multiple histogram method Date: Mon, 15 Nov 1999 13:14:49 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain Damn ... Please change t-t_o to t+t_o beloe > ---------- > From: Jan Reimers[SMTP:janr@molienergy.bc.ca] > Sent: Monday, November 15, 1999 12:32 PM > To: 'kynn@panix.com' > Cc: 'CHEMISTRY@ccl.net'; 'amf@arches.uga.edu' > Subject: CCL:[Q] Multiple histogram method > > One thing that helps is to further average over all possible origins in > time > (t_o) as follows > > ^+ > I think it is also better to use the differential form: > > Average over t_o {(-^2)/(-^2)} = exp(-t/tau) ^+ > solve for tau for various small values of t. Once t gets large the > average > will fluctuate around zero and you cannot use these numbers. > > I have copied Alan Ferrenberg in case he wants to add anything. > > Hope this helps. > > JR > > > ---------- > > From: kynn@panix.com[SMTP:kynn@panix.com] > > Sent: Friday, November 12, 1999 5:35 PM > > To: CHEMISTRY@ccl.net > > Subject: CCL:[Q] Multiple histogram method > > > > > > > > > > > > > > Several works (e.g. [1, 2]) reporting multiple histogram techniques to > > construct a free-energy surface, use a formulas containing a factor g, > > which equals (1 + 2*tau), where \tau is referred to as the "integrated > > correlation time". The exact definition of tau is given in pp. 33-34 > > of [3], and amounts to the integral with respect to t from 0 to > > infinity of - ^2 divided by the variance of A, where A > > is some quantity of interest. I have tried to obtain numerically the > > tau used in the multiple histogram techniques, but no matter how much > > data I amass, I still end up with something that doesn't come even > > close to converging (i.e. the integral above fluctuates widely > > throughout as one lets the upper limit of integration grow to > > infinity). > > > > Does anybody know where I can find more info on how to compute this tau? > > > > Thanks! > > > > KJ > > > > [1] Ferrenberg, A. M. and Swendsen, R. H. "Optimized Monte Carlo Data > > Analysis", 1989, Phys. Rev. Lett. 63(12) 1195-1198. > > > > [2] Kumar, S., et al. "The Weighted Histogram Analysis Method for > > Free-Energy Calculations on Biomolecules. I. The Method", 1992, > > J. Comp. Chem., 13(8) 1011-1021. > > > > [3] Binder, K. and Heermann, D. W. "Monte Carlo Simulation in > > Statistical Physics", 2nd Corr. Ed., 1992, pp. 33-34. > > > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > > Admins > > 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 > > > > > > > > > > > > -= 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 Mon Nov 15 16:36:23 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA26178 for ; Mon, 15 Nov 1999 16:36:23 -0500 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id NAA26718 for ; Mon, 15 Nov 1999 13:27:36 -0800 (PST) Date: Mon, 15 Nov 1999 13:27:36 -0800 (PST) From: "Dale A. Braden" To: cclpost Subject: Re: CCL:Two options in SCRF calculation of G98 In-Reply-To: <382FE413.A708260D@guomai.sh.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Yubo, One way to do it is: # b3lyp/6-31g* opt scrf=dipole (CH3)2S 0 1 3.64 6.2 where the cavity size and dielectric constant are read after the molecule specification, and another way is: # b3lyp/6-31g* opt scrf(dipole,a0=3.64,dielectric=6.2) (CH3)2S 0 1 where you specify a0 and dielectric in the route line. Good luck, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu On Mon, 15 Nov 1999, Yubo Fan wrote: > Hi, > > I am doing some G98W calculation including solvent effects. When I used > the keyword SCRF, I found two new dipole model options(A0=val and > Dielectric=val). I read the manual carefully and I still don't > understand how to use them. For example, if dimethyl sulfide molecule is > > wanted to be optimized on the level of B3LYP/6-31G* in dimethyl sulfide > solution (A0=3.64 angstrom, Dielectric=6.2), how should I write the > route section line? Please give me the > detail line. Thank you very much. > > Sincerely yours > > Y. Fan > > -- > ============================================================= > Yubo Fan Email: yubofan@guomai.sh.cn > Organic Synthesis Lab > The Department of Chemistry > Fudan University Phone: 8621-65648139 > No. 220 Handan Road Fax: 8621-65641740 > Shanghai, 200433 > P. R. China > ============================================================= > > > > > > -= 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 Mon Nov 15 18:31:24 1999 Received: from mailgw.cica.es (erika.cica.es [150.214.1.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA26926 for ; Mon, 15 Nov 1999 18:31:23 -0500 Received: from asterix.cica.es (asterix.cica.es [150.214.1.8]) by mailgw.cica.es (8.9.1/8.9.3) with ESMTP id AAA11491; Tue, 16 Nov 1999 00:22:34 +0100 (MET) Received: from localhost (localhost [[UNIX: localhost]]) by asterix.cica.es (8.8.8/8.8.8) with ESMTP id AAA18218; Tue, 16 Nov 1999 00:22:34 +0100 (MET) Date: Tue, 16 Nov 1999 00:22:33 +0100 (MET) From: Rafael Rodriguez Pappalardo To: Chris cc: ccl Subject: Re: CCL:acs-like bibtex style sheet? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi!, look for the achemso package in CTAN. Best regards Rafael -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (SPAIN) e-mail: rafapa@cica.es On Mon, 15 Nov 1999, Chris wrote: > hello, > > i am still discovering the joys of latex and bibtek. i am wondering if > anyone has a bibtex style for an american chemical society journal, i.e. > journal of physical chemistry? > > if you have such a style sheet, could you please send it to me? > > thanks, > chris > charwel@chthry.chem.lsu.edu > > > -= 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 Mon Nov 15 18:41:57 1999 Received: from sunflare.ccs.yorku.ca (sunflare.ccs.yorku.ca [130.63.236.128]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA26990 for ; Mon, 15 Nov 1999 18:41:57 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sunflare.ccs.yorku.ca (8.9.3/8.9.3) with SMTP id SAA02836 for <@mailrelay.yorku.ca:chemistry@ccl.net>; Mon, 15 Nov 1999 18:33:12 -0500 (EST) Received: by curl.gkcl.yorku.ca (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id SAA03014; Mon, 15 Nov 1999 18:38:01 -0500 From: chan@curl.gkcl.yorku.ca (Wai-To-Chan) Message-Id: <199911152338.SAA03014@curl.gkcl.yorku.ca> Subject: Ionization of a molecule... To: chemistry@ccl.net Date: Mon, 15 Nov 1999 18:38:00 -0500 (EST) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I am not sure about the nature of the 'potential barrier' to the detachment of an electron from an anion you refered to. The only such quantity that can measure such a barrier I know of is either the potential term from the Hartree-Fock one-electron equation or the one from the exact-one-electron schrodinger equation. You may find the discussion from Yang, Liu and Wang chem phys lett vol 258 pg 30 (1996) which shows how the ionization potential of an electron is related to the limit of the one-electron potential at infinite distance from a molecule relevant. In principle you can determine from visualization of distribution of the potential where an electron is 'forbidden' or 'allowed' as well as the barrier to removal of the electron in a molecule. But I highly doubt such information will be useful for spectroscopic measurement. If I am concerned with 'barrier' to ionization of an anion I will evaluate the intensity of the electron detachment spectrum (like calculating the Frank-Condon factor for an electronic excitation to determine how 'easy' a transition will take place) instead. I recall seeing reports of calculation of intensity of photo electron-detachment spectrum using some deconvolution method long ago but don't have any references handy with me. Email me if you are interested in any details. Wai-To Chan <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Is there a software package that will calculate the potential experienced by an electron as the parent molecule is ionized? I.e., calculate the energy as an electron is stepped further from the molecule (which is fixed in the optimized geometry). I am interested in determining the barrier as a polyanion is ionized. There is initially an attractive force holding the electron near the molecule. As the distance between the molecule (anion) and electron is increased, the dominant force becomes coulomb repulsion. Any references to published work would be appreciated. Roy Jensen >>>>>>>>>>>>>>>>>>>>>>>>>>>>