From chemistry-request@server.ccl.net Mon Dec 2 23:50:10 2002 Received: from smtp804.mail.sc5.yahoo.com ([66.163.168.183]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gB34oAO18375 for ; Mon, 2 Dec 2002 23:50:10 -0500 Received: from adsl-68-72-111-77.dsl.chcgil.ameritech.net (HELO localhost) (a-beim@sbcglobal.net@68.72.111.77 with plain) by smtp-sbc-v1.mail.vip.sc5.yahoo.com with SMTP; 3 Dec 2002 04:50:02 -0000 Date: Mon, 2 Dec 2002 22:49:44 -0600 Subject: Re: CCL:constrained multiple linear regression Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mime-Version: 1.0 (Apple Message framework v482) Cc: chemistry@ccl.net To: james.metz@abbott.com From: Geoff Hutchison In-Reply-To: Message-Id: X-Mailer: Apple Mail (2.482) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gB34oAO18378 On Monday, December 2, 2002, at 07:08 PM, james.metz@abbott.com wrote: >         I am looking for software (preferably free or inexpensive, code > is OK) that will allow me to perform > constrained multiple linear regression.  For example, I have an > equation of the form: >         Y = a*X1 + b*X2 + c*X3 + d I'm not certain if constrained regression is part of the base package, but I'd assume that the R statistical package can do this (among many, many other types of regression and other things). R is free and has been able to handle lots of thorny statistical problems I've thrown at it. http://www.r-project.org/ >         I must be able to constrain the range of values for a, b, c, > and d during the fitting. You might also try contacting the R project mailing list: r-help@lists.R-project.org -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.northwestern.edu/ From chemistry-request@server.ccl.net Tue Dec 3 03:09:54 2002 Received: from anor.ics.muni.cz ([147.251.4.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB389rO23144 for ; Tue, 3 Dec 2002 03:09:53 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by anor.ics.muni.cz (8.12.1/8.12.1) with ESMTP id gB389mRF015160 for ; Tue, 3 Dec 2002 09:09:48 +0100 Received: from ncbr.chemi.muni.cz (ncbr.chemi.muni.cz [147.251.28.55]) by bilbo.chemi.muni.cz (8.9.3/8.8.5) with ESMTP id JAA06084 for ; Tue, 3 Dec 2002 09:09:47 +0100 (MET) Received: from ncbr.chemi.muni.cz (ncbr.chemi.muni.cz [147.251.28.55]) by ncbr.chemi.muni.cz (8.11.3nb1/8.10.1) with ESMTP id gB389jJ10073 for ; Tue, 3 Dec 2002 09:09:45 +0100 (MET) Date: Tue, 3 Dec 2002 09:09:45 +0100 (MET) From: Jana Precechtelova To: "CCL.NET" Subject: CCL:g98-big displacement during the optimization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Muni-Virus-Test: Clean Dear CCL, does anyone have any idea conserning this problem?: I`m trying to perform a geometry optimization of a guanosine-cytidine base pair in G98 during which I freeze heavy atoms and optimize hydrogens (starting geometry is taken from experiment) but the problem is, even in the very first step of the optimization, the maximum displacement is terribly big and this remains the same during the whole optimization (see below the summary of the first step), which finally causes terminating of the opt. because of exceeding the number of steps. 1st step: Item Value Threshold Converged? Maximum Force 0.018320 0.000450 NO RMS Force 0.004048 0.000300 NO Maximum Displacement ******** 0.001800 NO RMS Displacement 8.056732 0.001200 NO last step: Item Value Threshold Converged? Maximum Force 0.000973 0.000450 NO RMS Force 0.000259 0.000300 YES Maximum Displacement ******** 0.001800 NO RMS Displacement 8.058591 0.001200 NO Predicted change in Energy=-1.508882D+03 Optimization stopped. -- Number of steps exceeded, NStep= 171 Thanks for any hint, Jana Precechtelova ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jana Precechtelova (MSc. student) NMR Laboratory National Centre for Biomolecular Research (NCBR) Faculty of Science, Masaryk University Kotlarska 2, 611 37 Brno, Czech Republic email: janap@ncbr.chemi.muni.cz phone: +420-5-41129588 fax: +420-5-411 29 506 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Tue Dec 3 04:14:26 2002 Received: from smtp.relc.com ([194.183.162.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB39ENO25772 for ; Tue, 3 Dec 2002 04:14:24 -0500 Received: from gw.imbg.org.ua (gw.imbg.org.ua [194.183.176.94]) by smtp.relc.com (8.12.6/8.12.6) with ESMTP id gB39EEJQ020221 for ; Tue, 3 Dec 2002 11:14:19 +0200 (EET) Received: from violet (violet.imbg.org.ua [10.0.5.80]) by gw.imbg.org.ua (8.12.6/8.11.6) with ESMTP id gB39TQXX011040 for ; Tue, 3 Dec 2002 11:29:26 +0200 (EET) (envelope-from dikov@imbg.org.ua) From: Dmitry Kovalsky Reply-To: dikov@imbg.org.ua Organization: IMBG To: Subject: Re: CCL:Cartesian vs DLC Date: Tue, 3 Dec 2002 11:13:55 +0200 User-Agent: KMail/1.4.7 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1251" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200212031113.55525.dikov@imbg.org.ua> X-AVP-RU: Passed Thanks to Mikael for the reply, I'm using PC GAMESS and doing 6-31 HF calculation. The beaviour of system and final structure better corresponds to crystal structure of the protein if the Cartesians are used. -- Sincerely yours, Ph.D. Student Dmitry Kovalsky Institute of Molecular Biology & Genetics 150 Akad. Zabolotnogo Street, Kiev-143, 03143 UKRAINE E-mail: dikov@imbg.org.ua Fax: +380 (44) 266-0759 Tel.: +380 (44) 266-5589 From chemistry-request@server.ccl.net Tue Dec 3 07:14:02 2002 Received: from moe.cs.uoguelph.ca ([131.104.96.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3CE2O09227 for ; Tue, 3 Dec 2002 07:14:02 -0500 Received: from daedalus.cs.uoguelph.ca (daedalus.cs.uoguelph.ca [131.104.96.102]) by moe.cs.uoguelph.ca (8.11.6/8.11.6) with ESMTP id gB3CDxZ17505; Tue, 3 Dec 2002 07:13:59 -0500 Received: (from wwwmgr@localhost) by daedalus.cs.uoguelph.ca (8.10.2+Sun/8.10.2) id gB3CDwt29920; Tue, 3 Dec 2002 07:13:58 -0500 (EST) Received: from 66.185.84.198 ( [66.185.84.198]) as user bilsmith@staff.mail.uoguelph.ca by webmail.uoguelph.ca with HTTP; Tue, 3 Dec 2002 07:13:58 -0500 Message-ID: <1038917638.3deca00637722@webmail.uoguelph.ca> Date: Tue, 3 Dec 2002 07:13:58 -0500 From: "William R. Smith" To: james.metz@abbott.com Cc: chemistry@ccl.net Subject: Re: CCL:constrained multiple linear regression References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 66.185.84.198 If you get stuck and can't find a stats package to do this, you are looking at a "nonlinear optimization problem" in general. Regression can be viewed as a special case of nonlinear optimization, and you should be able to find something in the literature of that field. If you use a least squares criterion, your problem is a "quadratic programming problem", and algorithms exist to solve it. For constrained problems like yours, a trick that sometimes works is to incorporating the constraints into a new expression, resulting in an unconstrained optimization problem (which many packages can handle). For your example, introduce the new (nonlinear) variable a1 and set a = a0 + (\epsilon_a)*sin(a1) where a0 is the mid-point of the constrained interval for a and \epsilon_a is its half- width. a1 is then the new nonlinear parameter. Quoting james.metz@abbott.com: > CCL, > > I am looking for software (preferably free or inexpensive, code is > OK) that will allow me to perform > constrained multiple linear regression. For example, I have an equation > of the form: > > Y = a*X1 + b*X2 + c*X3 + d > > where: Y is the dependent variable > X1 - X3 are independent variables (more than 1) > a, b, c are coefficients > d is a constant > > I must be able to constrain the range of values for a, b, c, and d > during the fitting. > > Please note that programs such as JMP, KalediaGraph, GraphPad > Prism, and several other packages do > NOT allow the user to do this, especially for more than one independent > variable. > > Can someone suggest a program or code to do this? > > Thank you, > Jim Metz > > > James T. Metz, Ph.D. > Research Investigator Chemist > > GPRD R46Y AP10-2 > Abbott Laboratories > 100 Abbott Park Road > Abbott Park, IL 60064-6100 > U.S.A. > > Office (847) 936 - 0441 > FAX (847) 935 - 0548 > > james.metz@abbott.com > -- Best Regards, W. R. Smith, Professor Dept. of Mathematics and Statistics, and School of Engineering Room 546 MacNaughton Building University of Guelph Stone Road and Gordon Streets Guelph, Ontario, CANADA N1G 2W1 Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; http://www.mathstat.uoguelph.ca/faculty/smith/ From chemistry-request@server.ccl.net Tue Dec 3 09:39:48 2002 Received: from curie.theoc.gu.se ([130.241.153.135]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3EdlO13037 for ; Tue, 3 Dec 2002 09:39:47 -0500 Received: from localhost (anan@localhost) by curie.theoc.gu.se (SGI-8.9.3/8.9.3) with ESMTP id PAA92637; Tue, 3 Dec 2002 15:37:47 +0100 (CET) Date: Tue, 3 Dec 2002 15:37:47 +0100 From: Anan Wu To: james.metz@abbott.com cc: chemistry@ccl.net Subject: Re: CCL:constrained multiple linear regression In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII If you can get access to Matlab, you will find a function called "fmincon". It fits into your problem very well. Anan Wu > CCL, > > I am looking for software (preferably free or inexpensive, code is > OK) that will allow me to perform > constrained multiple linear regression. For example, I have an equation > of the form: > > Y = a*X1 + b*X2 + c*X3 + d > > where: Y is the dependent variable > X1 - X3 are independent variables (more than 1) > a, b, c are coefficients > d is a constant > > I must be able to constrain the range of values for a, b, c, and d > during the fitting. > > Please note that programs such as JMP, KalediaGraph, GraphPad > Prism, and several other packages do > NOT allow the user to do this, especially for more than one independent > variable. > > Can someone suggest a program or code to do this? > > Thank you, > Jim Metz > > > James T. Metz, Ph.D. > Research Investigator Chemist > > GPRD R46Y AP10-2 > Abbott Laboratories > 100 Abbott Park Road > Abbott Park, IL 60064-6100 > U.S.A. > > Office (847) 936 - 0441 > FAX (847) 935 - 0548 > > james.metz@abbott.com > From chemistry-request@server.ccl.net Tue Dec 3 10:12:09 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3FC9O14069 for ; Tue, 3 Dec 2002 10:12:09 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 18FA191C7; Tue, 3 Dec 2002 16:12:09 +0100 (CET) To: chemistry@ccl.net, gamess-l@gl.ciw.edu Subject: Lanthanide ECP/Basis set Message-ID: <1038928329.3decc9c90bdb4@webmail.u-picardie.fr> Date: Tue, 03 Dec 2002 16:12:09 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, Dear Guenter Klatt, Rudolf Herrmann, Matt Thompson, Mark Russell, Concerning the HF SCF convergence problem of my Lanthanide derivative, it seems to depend on the starting structure. Using the ECP and Basis Set found in the following article: Cundari & Stevens, J.Chem.Phys. (1993) 98, 5555-5565, I wonder questions on the published Basis Set and its use in GAMESS... In GAMESS, this can be accomplished by using the "SBKJC" keyword to read the corresponding ECP and Basis set. I used the following input: GAMESS input: $CONTRL ECP=READ $END $BASIS GBASIS=SBKJC $END $DATA Samarium C1 Sm 62.0 0.00200 -0.10530 0.07010 etc... $END $ECP Sm-ECP SBKJC etc... $END I get the following information concerning the Samarium Basis Set used in the calculations (in the corresponding GAMESS ouput): .... SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENTS SM 1 L 1 12.6100000 -0.014999600000 -0.031579400944 1 L 2 3.2780000 0.718778800020 0.509098815215 1 L 3 2.2380000 -1.678150000046 -1.464062443754 2 L 4 0.8661000 1.000000000000 1.000000000000 3 L 5 0.3374000 1.000000000000 1.000000000000 4 L 6 0.0773200 1.000000000000 1.000000000000 5 D 7 0.7851000 0.379417690646 5 D 8 0.3622000 0.676914983311 6 D 9 0.1573000 1.000000000000 7 F 10 83.7600000 0.012467499970 7 F 11 30.5400000 0.087561599790 7 F 12 13.1600000 0.240539399422 7 F 13 5.7300000 0.420513498990 7 F 14 2.5850000 0.473468698863 8 F 15 1.1340000 0.747380677845 8 F 16 0.4445000 0.346313389734 ... I am quite surprised because the gaussians corresponding to D and F are NOT those found in the ORIGINAL paper i.e. in Cundari & Stevens, J.Chem.Phys. (1993) 98, page 5561. Moreover, I did not find in the GAMESS documentation some information for this modification. Now, if I built a new GAMESS input using the original publication values (i.e. without using the "SBKJC" keyword), GAMESS crashed: Here is my new input, writing the original D & F values: $CONTRL ECP=READ $END $SYSTEM MWORDS=2 $END $DATA Samarium C1 Sm 62.0 0.00200 -0.10530 0.07010 L 3 1 12.6100000 -0.014999600000 -0.031579400944 2 3.2780000 0.718778800020 0.509098815215 3 2.2380000 -1.678150000046 -1.464062443754 L 1 1 0.8661000 1.000000000000 1.000000000000 L 1 1 0.3374000 1.000000000000 1.000000000000 L 1 1 0.0773200 1.000000000000 1.000000000000 D 3 1 0.7851000 0.257405300000 2 0.3622000 0.459234000000 3 0.1573000 0.419376700000 F 7 1 83.7600000 0.009831000000 2 30.5400000 0.069045100000 3 13.1600000 0.189673000000 4 5.7300000 0.331588300000 5 2.5850000 0.373345200000 6 1.1340000 0.286865900000 7 0.4445000 0.132924900000 ... $END $ECP Sm-ECP GEN 46 3 2 ----- F POTENTIAL ----- -15.65862010 1 11.75812390 -6.05376496 1 2.32808297 3 ----- S-F POTENTIAL ----- -206.06726600 2 2.37776611 270.34259800 2 2.52471590 11.44490440 0 10.26438980 3 ----- P-F POTENTIAL ----- 10.69510070 0 10.00542360 121.87722800 2 2.20124125 -72.78839030 2 1.96809283 2 ----- D-F POTENTIAL ----- 29.52394000 2 2.06720439 9.03717701 0 6.71288904 ... $END Here is the crash message in the GAMESS ouput: ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD 1 0 0 -64.893260505 -64.893260505 69.831488803 0.000000000 ---------------START SECOND ORDER SCF--------------- 2 1 0 -38.064608925 26.828651581 56.444391313 0.714518144 SOSCF IS SCALING ROTATION ANGLE MATRIX, SQCDF= 0.199272 3 2 0 -44.283436820 -6.218827895 145.607000511 1.708186090 4 3 0 -40.786862178 3.496574642 121.005517556 1.274669095 SOSCF IS SCALING ROTATION ANGLE MATRIX, SQCDF= 0.104350 5 4 0 -46.700203112 -5.913340934 79.885738711 1.694913910 SOSCF ENCOUNTERS A SERIOUS PROBLEM IN -SONEWT- THE ROTATION ANGLE VECTOR HAS A HUGE NORM, SQCDF= 3.207E+00 REEXAMINE STARTING VECTORS, APPROPRIATENESS OF YOUR SCFTYP, ETC... EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Sun Dec 1 11:38:19 2002 453971 WORDS OF DYNAMIC MEMORY USED STEP CPU TIME = 0.78 TOTAL CPU TIME = 5.5 ( 0.1 MIN) TOTAL WALL CLOCK TIME= 7.2 SECONDS, CPU UTILIZATION IS 76.71% *** ERROR TERMINATION *** IN COMPUTE PROCESS 0 Why the GAMESS default values for D & F gaussians are NOT those that are published by Cundari et al.? Why does GAMESS crash with the original Cundari et al. values ? (I guess both problems are linked, the problem is that I did NOT find any information in the GAMESS documentation detailing this) Thanks, Regards, Francois From chemistry-request@server.ccl.net Tue Dec 3 11:25:19 2002 Received: from gate-sl1.mdli.com ([208.200.221.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3GPIO16212 for ; Tue, 3 Dec 2002 11:25:19 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id IAA21744 for ; Tue, 3 Dec 2002 08:25:18 -0800 (PST) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1 via smap (V2.1) id xma021707; Tue, 3 Dec 02 08:25:10 -0800 Received: from exch-sl02.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id IAA02262; Tue, 3 Dec 2002 08:25:09 -0800 (PST) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2653.19) id ; Tue, 3 Dec 2002 08:25:10 -0800 Message-ID: From: Keith Taylor To: Computational Chemistry List Subject: V3000 molfile format Date: Tue, 3 Dec 2002 08:23:59 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" If you use molfiles to transport structure information between applications, you need to be aware that MDL is introducing an enhancement to its stereochemical representation and this has an impact on the format of the molfile. The enhanced stereochemical representation will require the use of V3000 format molfiles and your molfile readers and writers will need to be updated to handle this information. MDL publishes the molfile format and the latest version of the document (August 2002) can be downloaded from: http://www.mdl.com/downloads/ctfile/ctfile_subs.html From chemistry-request@server.ccl.net Tue Dec 3 11:41:54 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3GfrO16848 for ; Tue, 3 Dec 2002 11:41:54 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18JG7N-0002hI-00; Tue, 03 Dec 2002 17:41:53 +0100 Message-ID: <3DECDE9C.7010902@mpi-bpc.mpg.de> Date: Tue, 03 Dec 2002 17:41:00 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: CCL , amber Subject: freeware for RNA modeling on Linux Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Does anyone know a good freeware (or cheap software --academic use) for RNA modeling. I have an RNA stem and I would like to attach a loop to it. Thanks alot, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@server.ccl.net Tue Dec 3 13:49:36 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3InZO20162 for ; Tue, 3 Dec 2002 13:49:35 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Tue, 03 Dec 2002 13:49:35 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Tue, 03 Dec 2002 13:49:12 -0500 From: "Peter Gannett" To: , , Subject: Re: CCL:freeware for RNA modeling on Linux Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gB3InaO20163 Vlad: I'm not sure what you mean... If you mean building the RNA you might look at McSym ( http://www-lbit.iro.umontreal.ca/mcsym/ ) which is specifically designed for RNAs. Alternatively, NAB (http://www.scripps.edu/case/casegr-sh-2.2.html ) can also do what you want. Both are free. If you want to do Molecular Mechanics/Dynamics, then NAMD ( http://www.ks.uiuc.edu/Research/namd/ ) can do the calculations and VMD ( http://www.ks.uiuc.edu/Research/vmd/ ) is a good viewer for the results. Both packages are free. As an alternative to NAMD, amber ( http://www.amber.ucsf.edu/amber ) can do the MM/MD and is very inexpensive for an academic site. Pete Gannett >>> Vlad Cojocaru 12/03/02 11:41AM >>> Does anyone know a good freeware (or cheap software --academic use) for RNA modeling. I have an RNA stem and I would like to attach a loop to it. Thanks alot, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Dec 3 12:36:43 2002 Received: from smtp.uh.cu ([216.72.24.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3HabO18307 for ; Tue, 3 Dec 2002 12:36:41 -0500 Received: from fq.uh.cu (canaria.qct.fq.oc.uh.cu [192.168.3.4]) by smtp.uh.cu (Postfix) with ESMTP id CB9EE34378 for ; Tue, 3 Dec 2002 13:36:10 -0500 (CST) Received: from Yigni (espectro.qct.fq.oc.uh.cu [192.168.3.44]) by fq.uh.cu (8.9.0/8.8.7) with SMTP id MAA23524 for ; Tue, 3 Dec 2002 12:37:44 -0500 Message-Id: <200212031737.MAA23524@fq.uh.cu> From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" Organization: =?ISO-8859-1?Q?Qu=EDmica_-_F=EDsica?= To: CHEMISTRY@ccl.net Date: Sun, 3 Dec 2000 12:35:39 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: rotational barrier Priority: normal In-reply-to: <200212021812.NAA07787@fq.uh.cu> References: <200212021856.20773.dikov@imbg.org.ua> X-mailer: Pegasus Mail for Windows (v3.01d) First i want to apologize me for the previous message that not had the required clarity. I'm trying to build the parameters for a MD simulation of an epoxidic sistem but a have not found any experimental data of the rotational barrier for the dihedral angle formed for the carbons 1,2,3 and any hydrogen bonded to carbon 3 in the 1,2-epoxypropane. I'll be grateful of any suggestion. _____________________________________________ Reynier Suardiaz del Rio Department of Physical Chemistry Chemistry Faculty University of Havana email: reynier@fq.uh.cu, reynier_s@yahoo.com _____________________________________________ From chemistry-request@server.ccl.net Tue Dec 3 14:23:25 2002 Received: from f04n01.cac.psu.edu ([128.118.141.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3JNOO21037 for ; Tue, 3 Dec 2002 14:23:24 -0500 Received: from psu.edu (cornea.chem.psu.edu [128.118.172.87]) by f04n01.cac.psu.edu (8.9.3/8.9.3) with ESMTP id OAA62662 for ; Tue, 3 Dec 2002 14:23:24 -0500 Message-ID: <3DED04AE.AEB8F92E@psu.edu> Date: Tue, 03 Dec 2002 14:23:26 -0500 From: Ed Brothers Reply-To: enb108@psu.edu Organization: PSU Merz Group X-Mailer: Mozilla 4.61 (Macintosh; I; PPC) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: First derivative of density matrix using CPHF. Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 8bit I am trying to construct the first derivative of the density matrix with respect to an atomic center's perturbation. I am able to solve the CPHF and I believe I am getting the right answers, but I am getting stuck on forming the first derivative of the density matrix. For the test case I am using an H2 with one uncontracted Gaussian with orbital exponent=3 on each atom. The optimized geometry and MO coefficients follow: H 0.116439735 0.116439735 0.116439735 H -0.116439735 -0.116439735 -0.116439735 c[ 1, 1]= -0.5937423229 c[ 2, 1]= -0.5937423229 = c[ 1, 1] c[ 1, 2]= 0.9271342977 c[ 2, 2]= -0.9271342977 = - c[ 1, 2] Where c[i,j] is AO i’s contribution to MO j. According to Pople, Krishnan, and Binkley, Int. J. Quant. Chem 13, 225-241 (1979), The first derivative of density matrix element u,v (Called D(u,v) below) is: dD(u,v)/dy = (Sum over r=1,2N) (Sum over S=1,2N) P’(r,s) c[u,r] c[v,s] Where N is the total number of basis functions, and r,s are over MO’s. If we assume the UHF case and an alpha density matrix, u and v are both alpha functions and r and s are only over alpha MO’s. Also, for this basis set there are only two alpha MO’s. Thus: dD(u,v)/dy = (Sum over r=1,2) (Sum over S=1,2) P’(r,s) c[u,r] c[v,s] dD(u,v)/dy = P’(1,1) c[u,1] c[v,1] + P’(1,2) c[u,1] c[v,2] + P’(2,1) c[u,2] c[v,1] + P’(2,2) c[u,2] c[v,2] My problem arises if we look at the derivative of density matrix elements 1,1 and 2,2. It would seem to me that for an arbitrary Cartesian perturbation, dD(1,1)/dy = dD(2,2)/dy. For instance, if this molecule was along the x-axis and we took the derivative of Atom 1 in the x direction, both D(1,1) and D(2,2) would change by the same amount. This doesn’t appear to be the case from my understanding of the mathematics, which indicates I am making an error somewhere. The derivative are formally: dD(1,1)/dy = P’(1,1) c[1,1] c[1,1] + P’(1,2) c[1,1] c[1,2] + P’(2,1) c[1,2] c[1,1] + P’(2,2) c[1,2] c[1,2] dD(2,2)/dy = P’(1,1) c[2,1] c[2,1] + P’(1,2) c[2,1] c[2,2] + P’(2,1) c[2,2] c[2,1] + P’(2,2) c[2,2] c[2,2] Now P’(1,1) is occupied-occupied, P’(2,1) and P’(1,2) are virtual-occupied, and P’(2,2) is virtual-virtual. According to equation (54) of Pople et. al., P’(occ,occ) = - S’(occ,occ) P’(occ,virt) = u(occ:virt) where the occ-virt is a single index and u is the result of the CPHF equation. P’(virt,virt) = 0. Thus the derivatives reduce to: dD(1,1)/dy = -S’(1,1) c[1,1] c[1,1] + 2u(2:1) c[1,1] c[1,2] dD(2,2)/dy = -S’(1,1) c[2,1] c[2,1] + 2u(2:1) c[2,1] c[2,2] (Note: I assume that P’(1,2) = P’(2,1). Is this correct?) We saw above that c[ 2, 1]= c[ 1, 1] and c[ 2, 2]= - c[ 1, 2]. If we substitute this into the relation ship for dD(2,2)/dy we get: dD(1,1)/dy = -S’(1,1) c[1,1] c[1,1] + 2u(2:1) c[1,1] c[1,2] dD(2,2)/dy = -S’(1,1) c[1,1] c[1,1] - 2u(2:1) c[1,1] c[1,2] And these are very obviously not equal. Does anyone know what I am doing wrong? Any assistance would be greatly appreciated, as I think this is a fairly trivial problem and I am stumped. Ed Brothers. Merz Group. PSU. PS Sorry about the length of the post. From chemistry-request@server.ccl.net Tue Dec 3 17:36:32 2002 Received: from mailrelay2.lanl.gov ([128.165.4.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3MaVO26903 for ; Tue, 3 Dec 2002 17:36:31 -0500 Received: from swan.lanl.gov (localhost.localdomain [127.0.0.1]) by mailrelay2.lanl.gov (8.12.3/8.12.3/(ccn-5)) with ESMTP id gB3MaRgp005635; Tue, 3 Dec 2002 15:36:27 -0700 Received: from heron.lanl.gov (heron.lanl.gov [128.165.96.39]) by swan.lanl.gov (8.12.1/8.12.1) with ESMTP id gB3NZoFj021608; Tue, 3 Dec 2002 16:35:50 -0700 Received: from localhost (tamulis@localhost) by heron.lanl.gov (8.12.1/8.12.1) with ESMTP id gB3FVgJp001664; Tue, 3 Dec 2002 08:31:42 -0700 Date: Tue, 3 Dec 2002 08:31:42 -0700 (MST) From: "Temporary Guest Account;CNLS;7-1444;9999999" To: cc: , Subject: Negative values of HFS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, would you please to explain what does it means the negative values of Isotropic Fermi Contact Couplings constants calculated by G98 A.13.3 Enclosed please find part of resulting file: Atom a.u. MegaHertz Gauss 10(-4) cm-1 6 N(14) 0.10574 34.16484 12.19087 11.39616 17 O(17) 0.06247 -37.87121 -13.51339 -12.63247 Thanks in advance. Regards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Temporal address until 28 February 2003: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: (505) 667-7278 Fax: (505) 665-2659 e-mail: tamulis@cnls.lanl.gov *******************************************************************