From chemistry-request@server.ccl.net Tue Nov 14 00:47:01 2000 Received: from keeper.ludwig.edu.au (keeper.ludwig.edu.au [128.250.250.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA03773 for ; Tue, 14 Nov 2000 00:46:58 -0500 Received: from ludwig.edu.au (proxy.ludwig.edu.au [128.250.250.3]) by keeper.ludwig.edu.au with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id VD9R874X; Tue, 14 Nov 2000 16:46:38 +1100 Sender: jorissen@ccl.net Message-ID: <3A10D1C2.3EACDBF5@ludwig.edu.au> Date: Tue, 14 Nov 2000 16:46:42 +1100 From: Robert Jorissen Organization: Ludwig Institute for Cancer Research X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: help with MMFF94 in CHARMM Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello I wish to perform some calculations using the MMFF94 forcefield in CHARMM. (I am using the acedemic version 25b1). I calculated the energies of a small number of small molecules from the MMFF94 validation set. Although the energy components from the bonded parameters (bond stretch, angle bending etc) seem to agree with those listed in the Batchmin and Optimol log files provided as part of the validation set files, I seem to have slight discrepencies with the van der Waals energies in some (but not all) of the systems and with the electrostatic energies in all of the small number of systems I have looked at so far. The results for one molecule are shown below. (Easy to compare the numbers if Courier font is used to view them.) The results from each energy term are from my CHARMM calculation, the calculation using Optimol and the calculations using Batchmin in double precision and single precision respectively. I would appreciate hearing from anyone who has used the MMFF94 forcefield in CHARMM and whether they encountered this problem. I doubt that this can be explained by numerical imprecision in calculation since calculations "by hand" using a spreadsheet yield values for the electrostatic energy far closer to the Optimol and Batchmin values than the values I calculated using CHARMM. Also, the partial charges produced by CHARMM agreed with those in the input coordinate files. Any assistance would be appreciated. Rob BEWCUB - 18-ACETATO-ASPARENOMYCIN A P-NITROBENZYL ESTER "?BOND" to "4.74997" Optimol: 4.74997 BMin DP: 4.74997559238 BMin SP: 4.749975 "?ANGL" to "20.6828" Optimol: 20.68285 BMin DP: 20.6828388838 BMin SP: 20.68284 "?DIHE" to "24.6512" Optimol: 24.65119 BMin DP: 24.6511913190 BMin SP: 24.65120 "?OOPL" to "-4.39081" Optimol: -4.39082 BMin DP: -4.39081620274 BMin SP: -4.390817 "?STRB" to "0.136841" Optimol: 0.13684 BMin DP: 0.136842257168 BMin SP: 0.1368436 "?ELEC" to "-41.184" Optimol: -41.40216 BMin DP: -41.4021642936 BMin SP: -41.40216 "?VDW" to "48.2924" Optimol: 48.18183 BMin DP: 48.1818461796 BMin SP: 48.18185 "?ENER" to "52.9385" Optimol: 52.60970 BMin DP: 52.6097137356 BMin SP: 52.60972 -- ----------------------------------------------------- Robert Jorissen Ludwig Institute for Cancer Research P.O. BOX 2008, Royal Melbourne Hospital Parkville, Victoria 3050, Australia phone: ++61-3-9341-3155 fax: ++61-3-9341-3104 e-mail: Robert.Jorissen@ludwig.edu.au WWW: http://modelling.ludwig.edu.au/~jorissen/ ----------------------------------------------------- From chemistry-request@server.ccl.net Tue Nov 14 04:05:27 2000 Received: from silver.ch.unito.it (silver.ch.unito.it [130.192.118.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA04773 for ; Tue, 14 Nov 2000 04:05:26 -0500 Received: from chpc47.ch.unito.it (chpc47.ch.unito.it [130.192.118.47]) by silver.ch.unito.it (8.9.3/8.9.3) with SMTP id KAA05663 for ; Tue, 14 Nov 2000 10:20:57 +0100 (MET) Message-Id: <3.0.3.32.20001114100410.007be920@silver.ch.unito.it> X-Sender: teorica@silver.ch.unito.it X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Tue, 14 Nov 2000 10:04:10 +0100 To: chemistry@ccl.net From: Theoretical Chemistry Group Subject: Re: CCL:Ice Structure Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" You can look at http://www.ch.unito.it/ifm/teorica/compounds.html Theoretical Chemistry Group University of Torino Via Giuria 5 - I 10125 Torino Italy Phone: +39 011 670 7564 Fax: +39 011 670 7855 E mail teorica@ch.unito.it >At 18.09 07/11/00 +0530, you wrote: >>Hi All, >> >>Does anybody know the references for X-ray crystal structural >>parameters as well as theoretically calulated structures for Ice? >> >>With thanks, >> >>Dr. Tapan K. Ghanty >>Chemistry Division >>BARC, Trombay >>Mumbai 400 085 >>India > From chemistry-request@server.ccl.net Tue Nov 14 05:24:30 2000 Received: from lithium.theochem.uni-duesseldorf.de (lithium.theochem.uni-duesseldorf.de [134.99.82.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA05097 for ; Tue, 14 Nov 2000 05:24:29 -0500 Received: from borussia.theochem.uni-duesseldorf.de (borussia.theochem.uni-duesseldorf.de [134.99.82.13]) by lithium.theochem.uni-duesseldorf.de (8.11.1/8.11.1) with ESMTP id eAEAODi17503; Tue, 14 Nov 2000 11:24:14 +0100 Received: from localhost (localhost [[UNIX: localhost]]) by borussia.theochem.uni-duesseldorf.de (8.11.1/8.11.1) id eAEAODo01269; Tue, 14 Nov 2000 11:24:13 +0100 From: Wibke Sudholt Reply-To: wibke@theochem.uni-duesseldorf.de To: CHEMISTRY@ccl.net Subject: Excited State Reviews Date: Tue, 14 Nov 2000 10:57:32 +0100 X-Mailer: KMail [version 1.0.29] Content-Type: text/plain Cc: wibke@theochem.uni-duesseldorf.de MIME-Version: 1.0 Message-Id: <00111411241301.01255@borussia> Content-Transfer-Encoding: 8bit Dear CCLers, I'm looking for review papers and/or key articles and/or web pages about the quantum chemical calculation of electronically excited states (especially singlet excited states). I'm interested in organic molecules with about 10 heavy atoms (about 20 atoms in total). The question I would like to answer is: Which semiempirical/ab initio/density functional methods are known for this purpose? How expensive and accurate are they? I'm aware of the CASSCF/CASPT2 articles of Roos et al. and also of some papers about CIS, TDDFT, DFT/SCI and DFT/MRCI. Thank you very much in advance! Best regards Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de From chemistry-request@server.ccl.net Tue Nov 14 07:20:51 2000 Received: from hermes.csd.unb.ca (root@hermes.csd.unb.ca [131.202.3.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06611 for ; Tue, 14 Nov 2000 07:20:50 -0500 Received: from mailserv.unb.ca (root@mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.9.3/8.9.3) with ESMTP id IAA12476; Tue, 14 Nov 2000 08:20:39 -0400 (AST) Received: from bongo (bongo.chem.unb.ca [131.202.162.240]) by mailserv.unb.ca (8.8.8+Sun/8.8.8) with SMTP id IAA21134; Tue, 14 Nov 2000 08:20:39 -0400 (AST) Message-Id: <3.0.6.32.20001114082120.00883b10@newpop.unb.ca> X-Sender: ajit@newpop.unb.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 14 Nov 2000 08:21:20 -0400 To: Eric Scerri From: "Ajit J. Thakkar" Subject: CCL: Re: Hund's rules Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Eric Scerri wrote: >>Can Hund's rule of maximum multiplicity be derived from quantum mechanics or is it still to be considered as the summary of experimental results? Hund's rule of maximum multiplicity is not rigorous --- experimental cases where it breaks down are rare but known. Within the restricted Hartree-Fock approximation, the rule is exact and in fact the energy difference can be shown to lie between between multiples of (positive) exchange integrals computed with the upper state orbitals and the same quantity computed with the lower state orbitals. For more details see: Colpa, Mol Phys 28 (1974) 581; Colpa, Thakkar, Smith and Randle, Mol Phys 29 (1975) 1861. Ajit -- Dr. Ajit J. Thakkar Professor Department of Chemistry Tel: 1-506-453-4629 University of New Brunswick Fax: 1-506-453-4981 Fredericton, NB E3B 6E2 E-mail: ajit@unb.ca Canada http://www.unb.ca/chem/ajit/ From chemistry-request@server.ccl.net Tue Nov 14 06:45:10 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA05603 for ; Tue, 14 Nov 2000 06:45:08 -0500 Received: (qmail 24937 invoked from network); 14 Nov 2000 11:44:51 -0000 Received: from titanas.chemistry.upatras.gr (150.140.180.134) by nic.upatras.gr with SMTP; 14 Nov 2000 11:44:51 -0000 Received: (qmail 7697 invoked from network); 14 Nov 2000 11:49:56 -0000 Received: from ariadne.chemistry.upatras.gr (HELO Ariadne) (150.140.180.140) by titanas.chemistry.upatras.gr with SMTP; 14 Nov 2000 11:49:56 -0000 Message-ID: <003201c04e32$5b6ee720$8cb48c96@chemistry.upatras.gr> From: "Menadakis Manolis" To: Subject: good forcefield for calcite? Date: Tue, 14 Nov 2000 13:59:35 +0200 Does anyone know where i can find a good forcefield for calcite? thanks! From chemistry-request@server.ccl.net Tue Nov 14 07:13:50 2000 Received: from lozen.uit.no (lozen.Uit.No [129.242.5.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06565 for ; Tue, 14 Nov 2000 07:13:49 -0500 Received: from james.chem.uit.no (james.Chem.Uit.No [129.242.24.111]) by lozen.uit.no (8.10.1/8.10.1) with ESMTP id eAECDcf14039 for ; Tue, 14 Nov 2000 13:13:38 +0100 (MET) Received: from chem.uit.no (IDENT:bolvin@neptun.Chem.Uit.No [129.242.24.168]) by james.chem.uit.no (8.9.3/8.9.3) with ESMTP id NAA216884 for ; Tue, 14 Nov 2000 13:14:37 +0100 (CET) Sender: bolvin@chem.uit.no Message-ID: <3A112DD5.C6B2AE22@chem.uit.no> Date: Tue, 14 Nov 2000 13:19:33 +0100 From: Helene BOLVIN X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: ROHF and SCRF in G98 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hallo everybody, I try to do some geometry optimization of open-shell molecules in solvent. The geometry optimization of the coresponding closed-shell molecules are without any problem, and the geometry optimization of the open-shell molecule without solvent runs without any problem as well. But I seems there is a problem in the calculation of the gradient when both ROHF and scrf=(cpcm,solvent=water) are used at the same time. I have experienced this with several molecules. The error message is the following: NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF- NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH INITIALIZATION PASS ************************************************ ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** ************************************************ Has someone an idea about what I have to do? Thanks in advance Helene BOLVIN -- ***************************************************************** Hélène BOLVIN Institutt for kjemi tlf: (+47) 77 64 40 61 Universitetet i Tromsø fax: (+47) 77 64 47 37 N-9037 TROMSØ ***************************************************************** From chemistry-request@server.ccl.net Tue Nov 14 09:18:13 2000 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07242 for ; Tue, 14 Nov 2000 09:18:08 -0500 Received: from dale.ri.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 14 Nov 2000 14:17:47 +0000 Received: from ri.ac.uk (davy.ri.ac.uk) by dale.ri.ac.uk (Content Technologies SMTPRS 4.1.5) with SMTP id for ; Tue, 14 Nov 2000 14:16:32 +0000 Received: from faraday.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA23901; Tue, 14 Nov 2000 14:17:45 GMT Received: from localhost by faraday.ri.ac.uk (980427.SGI.8.8.8) id OAA11661; Tue, 14 Nov 2000 14:17:45 GMT Date: Tue, 14 Nov 2000 14:17:44 +0000 (WET) From: Stefan Bromley X-Sender: stefan@faraday Reply-To: Stefan Bromley To: chemistry@ccl.net Subject: Dmol DOS files In-Reply-To: <3.0.3.32.20001114100410.007be920@silver.ch.unito.it> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am trying to analyse Dmol4.0 DOS (*.dos) files through either Cerius2 or InsightII. Cerius2, when going to DMOL and then analyse asks for extra restart files even though the *.dos file is present in the relevant directory and the only way it sems to continue is to rerun the job. InsightII gives an error message (going through Dmol -> Analysis) saying that the file format is wrong. In the past I have used InsightII to look at Dmol3.5 DOS files to look at projected density of states and Gaussian broadened total dos, etc but now the file format seems to have changed. Does anyone know how the file format has changed in order that I can use InsightII and/or does anyone know the necessary files needed to use the option in Cerius2. Many thanks for your help in advance. Stefan ________________________________________________________________________ Dr. S. T. Bromley Royal Institution of Great Britain Phone: +44 (0)171-409-2992 Registered Charity Number 227938 Fax: +44 (0)171-629-3569 Davy Faraday Research Laboratory email: stefan@ri.ac.uk 21 Albemarle Street LONDON W1X 4BS, UK ________________________________________________________________________ ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This footnote also confirms that this email message has been swept by MIMEsweeper for the presence of computer viruses. www.mimesweeper.com ********************************************************************** From chemistry-request@server.ccl.net Tue Nov 14 11:00:21 2000 Received: from facstaff01.udayton.edu (facstaff01.udayton.edu [131.238.75.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07893 for ; Tue, 14 Nov 2000 11:00:20 -0500 From: Melinda.Greer@notes.udayton.edu Subject: nominations for Patterson-Crane award To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-ID: Date: Tue, 14 Nov 2000 11:00:07 -0500 X-MIMETrack: Serialize by Router on FacStaff01/SVR/UDayton(Release 5.0.5 |September 22, 2000) at 11/14/2000 11:00:07 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii CALL FOR NOMINATIONS American Chemical Society Award Nominees for the 2001 Patterson-Crane Award are being sought by the Dayton and Columbus, Ohio Sections of the American Chemical Society. The biennial award, consisting of a $2000 honorarium and a personalized commendation, is given in honor of Austin M. Patterson and E. J. Crane, previous editors of Chemical Abstracts. An international honor, the Patterson-Crane Award acknowledges outstanding contributions to the field of chemical information, including the design, development, production or management of chemical information systems or services; electronic access and retrieval of chemical information; critically evaluated data compilations; information technology applications in chemistry; or other significant chemical documentation. Nominations for the award must be in writing and should discuss the nominee's contributions to the field and provide an evaluation of accomplishments. Materials supporting the nomination should include a biography and bibliography of publications and presentations relevant to the award. Seconding letters are required. Send one copy of the nomination materials to The Patterson-Crane Award Committee, Melinda Greer, Chair, University of Dayton Chemistry Department, 300 College Park, Dayton, OH 45469-2357, for receipt by 31 January 2001. For more detailed information, see the ACS Dayton Section web page ( http://www.udayton.edu/~acs) or contact Melinda Greer at (937) 229-2666 or melinda.greer@notes.udayton.edu. Nominations will be judged by a seven-member selection committee consisting of Dayton and Columbus Section members as well as the Chair of the American Chemical Society Division of Chemical Information. The 2001 Patterson-Crane Award will be presented 8 May 2001 at an awards dinner to be held in Dayton, Ohio. From chemistry-request@server.ccl.net Tue Nov 14 13:53:02 2000 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 NAA08596 for ; Tue, 14 Nov 2000 13:53:01 -0500 Received: from roswell.ks.uiuc.edu (roswell.ks.uiuc.edu [130.126.120.132]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id MAA28800 for ; Tue, 14 Nov 2000 12:52:46 -0600 (CST) Received: from localhost (emad@localhost) by roswell.ks.uiuc.edu (8.9.1b+Sun/8.9.1) with ESMTP id MAA29270 for ; Tue, 14 Nov 2000 12:52:46 -0600 (CST) X-Authentication-Warning: roswell.ks.uiuc.edu: emad owned process doing -bs Date: Tue, 14 Nov 2000 12:52:46 -0600 (CST) From: Emad Tajkhorshid To: ccl CCL Subject: Summary: Different platforms for QM ... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I would liek to thank all people who replied to my question. here is a summary. Original Question: > I wonder if anybody has efficiently used SUN platforms for running quantum > chemical calculations, e.g. Gaussian9x. We are considering to purchase a > new machine for our group particularly for quantum chemical calculations. > Among our options are SUN and Alpha machines. Any comment or suggestion > with regard to this is appreciated. > **************************************************************************** Date: Thu, 09 Nov 2000 01:26:46 -0500 From: Deepak Singh We have had success running G94 on DEC-alpha machines. They were very fast. However, in my opinion alphas are not the most stable platform. While I have never used SUNS the reports are fairly good. A SUN ULTRA10 is a good machine to invest in. **************************************************************************** Date: Thu, 9 Nov 2000 08:59:23 +0100 From: Jens Abildgaard The sun machines usually sucked, but it has been a while since we tested them, so please send us details when you find out. Solaris (64 bit?) and UltraSpark (64 bit) with the "switched crossbar technology should on paper run well, but I have just never heard of anybody achiving that. I would consider IBM (Power3 chip!!!, and not the PowerPC running AIX) or HP (PA-RISC 8600 or similar with 64 bit HP-UX 11.0, and MLIB mathematical libraries). Remember to look at Prize/Performance, if you can afford it at all. Be aware that if you test LINUX boxes, you need a reasonable size problem, as small testjobs run very fast, while real size problems may easyly be a factor of 10 slower than the real UNIX machine **************************************************************************** Date: Thu, 9 Nov 2000 09:58:30 +0100 (MET) From: Frank Jensen I would be interested in knowing if anybody has a working SUN version of Gaussian-94 still around. I do have both Gaussian-98 and -94, but they are giving me some discrepancies in the SGI version. I have G98 running on a SUN machine, but the makefile for G94 is set up for SUN-OS 5 and compiler version 2, and I don't have access to that kind of vintage machines. Thus I would be interested in either a working set of executables for G94, or a G94 makefile for the more recent SUN-OS (7/8) and compilers (5/6). **************************************************************************** Date: Thu, 9 Nov 2000 09:48:05 +0000 (GMT) From: Bruce. Tattershall Our university has several timeshared Sun multiprocessor machines running unix. Details may be found at http://www.ncl.ac.uk/ucs/computers.html We have used g94 and now g98 on these, essentially using spare capacity via dnqs. Performance is excellent for my purposes: geometry optimisation of a 67 atom molecule with no symmetry (39 non-H atoms, including a P4S3 cage and four fused organic rings) took 4 days of cpu time using one processor of the fastest of these, at the MPW1PW91/Ahlrichs SVP level. Considerable experiment or expertise is needed to screw up the optimisation level by using appropriate compilation parameters, to achieve this on a particular installation. We have found that support from Gaussian leaves quite a bit to be desired: in particular, while the main suite of Gaussian routines work as intended, we believe, several of the utility programs, e.g. formchk, do not work at all. These are installation-dependent bugs which Gaussian has said they will work on, but as far as we know, still have not cured. **************************************************************************** Date: Thu, 09 Nov 2000 07:09:43 +0000 From: jmmckel@attglobal.net Any predujices against Athlon or Intel machines? An 800MHZ PIII Dell costs ~$1400, and runs Gaussian just fine. John McKelvey **************************************************************************** Date: Thu, 10 Nov 2000 11:32:21 -0500 (EST) From: Sergei Tretiak Dear Emad, I have some experience of running G9X on Alpha (dual 21264 666 MHz box), PC (dual Intel PIII 800 MHz box) and Sun (4-CPU 600MHz box). My impression is: 1. Alpha is the champ. It is in average 1.5 times faster then Sun and has reasonable price/performance ratio; easy to configure and compile G9X. Go for Linux box with Compaq compiler suit. It performance is on par with native Unix64 OS (but a lot cheaper). 2. PC is extremely fast and extremely cheap. Its speed is on par with Sun and PC has the best price/performance ratio. However, building PC requires carefull choice of hardware (e.g. SCSI configuration, good motherboard and memory, etc.) and software (e.g. PGI compiler and optimized BLAS for G9X compilation). Also PC has limit on RAM (about 1-1.5 GB) and # of CPUs (2). 3. There is no reason to buy Sun for quantum chemical calculations (unless there are other motives). It is not faster then PC and very expensive. Compilation of G9X could be a headache. **************************************************************************** Emad ------------------ Emad Tajkhorshid http://www.ks.uiuc.edu/~emad Theoretical Biophysics Group Beckman Institute for Advanced Science and Technology 405 N. Mathews, Urbana, IL 61801 Tel: (217)244-5042 Fax: (217)244-6078 Email: emad@ks.uiuc.edu From chemistry-request@server.ccl.net Tue Nov 14 14:39:54 2000 Received: from t12mail.lanl.gov (t12mail.lanl.gov [128.165.22.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08926 for ; Tue, 14 Nov 2000 14:39:53 -0500 Received: from lanl.gov (gold.lanl.gov [128.165.22.10]) by t12mail.lanl.gov (8.9.1a/8.9.1) with ESMTP id MAA09030 for ; Tue, 14 Nov 2000 12:39:54 -0700 (MST) Sender: tymczak@t12mail.lanl.gov Message-ID: <3A11A319.A3986DCB@lanl.gov> Date: Tue, 14 Nov 2000 13:39:53 -0700 From: "C. J. Tymczak" Organization: LANL X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Quantum Chemistry Codes/ crystal Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone now how to in the crystal code? 1) Turn off the K-space sums 2) Use a specific box geometry, specifically a cubic box with one atom in it And what density functional is it using ???? Also, does anyone out there know of any public domain software which is easy to use and does Electronic structure calculation in real space for periodic systems ??? ================================================= | Dr. C. J. Tymczak | | Group T-12 MS 268 | | Los Alamos National Laboratory | | Phone:(505)-667-3881 | ========================================================= From chemistry-request@server.ccl.net Tue Nov 14 16:44:50 2000 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA09962 for ; Tue, 14 Nov 2000 16:44:50 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id QAA25851 for ; Tue, 14 Nov 2000 16:44:48 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A11B2B5.1CADE1E6@cornell.edu> Date: Tue, 14 Nov 2000 16:46:30 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Another CHARMM question. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have a new CHARMM question/problem. I finally figured out the last one. This one goes like this. I have an image file and the coordinates for 512 TIP3P water molecules. I cn generate a box of 3456 TIP3P water molecules with the box being 24.8616 A on a side. My question is this: how can I generate a bigger box that has more water molecules in it? The box needs to be about 80 A or so (I'm trying to solvate a protein) Thanks to all of you for your suggestions and Thanks to Rick Venable and Michael Brunsteiner for their help with my last problem. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Tue Nov 14 17:21:11 2000 Received: from dogstar.duch.udel.edu (dogstar.duch.udel.edu [128.175.138.122]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA10207 for ; Tue, 14 Nov 2000 17:21:11 -0500 Received: from localhost (gijukt@localhost) by dogstar.duch.udel.edu (8.9.3/8.9.3) with ESMTP id RAA236930 for ; Tue, 14 Nov 2000 17:22:04 -0500 (EST) Date: Tue, 14 Nov 2000 17:22:04 -0500 From: Giju Thomas Kalathingal To: chemistry@ccl.net Subject: classical free energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Everybody, Could you please give me some references or suggestions on how to estimate classical free energy of formation of a molecule? Thanks in advance, Giju ____________________________________________________________ Giju T. Kalathingal Department of Chemistry and Biochemistry University of Delaware, Newark, Delaware 19716, USA. E-mail: gijukt@udel.edu URL: http://dogstar.duch.udel.edu/gijukt/welcome.html ____________________________________________________________