From chemistry-request@ccl.net Wed May 12 07:04:54 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4CC4rkh023723; Wed, 12 May 2004 07:04:53 -0500 To: Kerwin.D.Dobbs{at}usa.dupont.com Cc: chemistry{at}ccl.net, "Computational Chemistry List" Subject: Modelling Tools in Material Science details MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy{at}givaudan.com Date: Wed, 12 May 2004 14:06:56 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 12/05/2004 14:07:08, Serialize complete at 12/05/2004 14:07:08 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.5 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4CC4skh023727 Dear Colleagues, I wish to find alternatives of Cerius2 Modules as follows: Sorption tool, Mesoscale modelling, Blend, Synthia, DPD. I want to model small molecules-polymer intereactions, adsorption, diffusion, viscosity. I am interested both batch and frontend applications. Regards, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy{at}givaudan.com From chemistry-request@ccl.net Tue May 11 22:41:15 2004 Received: from schrodinger.com (thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4C3fEkh000546 for >ccl.net>; Tue, 11 May 2004 22:41:15 -0500 Received: from SVETLA (svetla.schrodinger.com [192.156.98.141]) by schrodinger.com (8.12.11/8.12.8) with SMTP id i4C3hFx7099597 for >ccl.net>; Tue, 11 May 2004 20:43:28 -0700 (PDT) (envelope-from announce<>schrodinger.com) From: Schrodinger Announcements >schrodinger.com> To: CCL >ccl.net> Subject: Schrodinger Meetings in CA, May 19-20 Date: Tue, 11 May 2004 23:40:29 -0400 Message-ID: <0511104234029.36@SVETLA> MIME-Version: 1.0 Content-type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.9 required=7.5 tests=IMPRONONCABLE_1,NO_COST autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4C3fFkh000552 Schrvdinger is hosting two seminars in California - Wednesday, May 19th, in San Francisco, and Thursday, May 20th, in San Diego - highlighting recent advances in drug design research. Methods development as well as real-world pharmaceutical applications will be presented. For a detailed listing of topics, please visit our web site: http://www.schrodinger.com/Announce/Workshop/W2004/ugmspring2004.html There is no charge for the seminars, but space is limited, so please register on-line in advance. From chemistry-request@ccl.net Wed May 12 10:27:45 2004 Received: from oulu.fi (ousrvr.oulu.fi [130.231.240.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4CFRfkh032461 for >ccl.net>; Wed, 12 May 2004 10:27:41 -0500 Received: from webmail.oulu.fi (webmail.oulu.fi [130.231.241.38]) by oulu.fi (8.12.10/8.12.10) with ESMTP id i4CFTuZm022981 for >ccl.net>; Wed, 12 May 2004 18:29:56 +0300 (EEST) Received: from webmail.oulu.fi (localhost.localdomain [127.0.0.1]) by webmail.oulu.fi (8.12.10/8.12.10) with ESMTP id i4CFTur3001990 for >ccl.net>; Wed, 12 May 2004 18:29:56 +0300 Received: (from apache@localhost) by webmail.oulu.fi (8.12.10/8.12.10/Submit) id i4CFTuNB001988 for chemistry<>ccl.net; Wed, 12 May 2004 18:29:56 +0300 Received: from yok187.oulu.fi (yok187.oulu.fi [130.231.4.187]) by webmail.oulu.fi (IMP) with HTTP for >koivu.oulu.fi>; Wed, 12 May 2004 18:29:56 +0300 Message-ID: <1084375796.40a242f4b33fa<>webmail.oulu.fi> Date: Wed, 12 May 2004 18:29:56 +0300 From: Satyan Sharma >sun3.oulu.fi> To: chemistry<>ccl.net Subject: ONIOM--help!! MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.3-cvs X-Originating-IP: 130.231.4.187 X-Spam-Status: No, hits=1.9 required=7.5 tests=IMPRONONCABLE_1, LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello everyone, Could somebody please explain me why I am getting this error (pasted below) while doing ONIOM calculation on a dipeptide. I have a GLY and an ASP, with -1 charge. The -CH2COO group is treated at higher level and rest at a lower level during optimization(the input file I am using is also attached). INPUT FILE FOR G03##### #P ONIOM(B3LYP/STO-3G:UFF) # Opt(Redundant,MaxCycle=5000) # Gfinput IOP(6/7=3) Test # Units(Ang,Deg) Input file -1 1 -1 1 0 1 N 0 0.162 -0.202 0.000 Low C 0 1.612 -0.031 -0.000 Low C 0 1.985 1.432 -0.000 Low O 0 1.137 2.319 -0.000 Low H 0 -0.299 -1.179 0.000 Low H 0 -0.513 0.641 -0.000 Low H 0 2.055 -0.519 0.888 Low H 0 2.055 -0.519 -0.888 Low N 0 3.274 1.699 -0.000 Low C 0 3.780 3.069 -0.000 Low H C 0 5.290 3.088 -0.000 Low O 0 5.976 2.019 0.000 Low C 0 3.191 3.859 1.198 High C 0 3.485 5.366 1.241 High O 0 3.748 5.964 2.273 High O 0 3.442 5.949 0.005 High H 0 3.934 0.845 0.000 Low H 0 3.455 3.526 -0.953 Low H 0 5.755 4.073 -0.000 Low H 0 2.096 3.734 1.257 High H 0 3.571 3.424 2.145 High ########TAIL PART OF LOG FILE################ Total kinetic energy from orbitals= 2.240279193651D+02 No NMR shielding tensors so no spin-rotation constants. Leave Link 601 at Wed May 12 17:25:01 2004, MaxMem= 65536000 cpu: 0.7 (Enter /mnt/mds/irix65_mips64/appl/chem/gaussian/G03RevB.02/g03/l701.exe) Compute integral first derivatives. ... and contract with generalized density number 0. Leave Link 701 at Wed May 12 17:25:02 2004, MaxMem= 65536000 cpu: 0.5 (Enter /mnt/mds/irix65_mips64/appl/chem/gaussian/G03RevB.02/g03/l702.exe) L702 exits ... SP integral derivatives will be done elsewhere. Leave Link 702 at Wed May 12 17:25:03 2004, MaxMem= 65536000 cpu: 0.0 (Enter /mnt/mds/irix65_mips64/appl/chem/gaussian/G03RevB.02/g03/l703.exe) Compute integral first derivatives, UseDBF=F. Integral derivatives from FoFDir, PRISM(SPDF). Symmetry not used in FoFDir. MinBra= 0 MaxBra= 1 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Leave Link 703 at Wed May 12 17:25:07 2004, MaxMem= 65536000 cpu: 4.4 (Enter /mnt/mds/irix65_mips64/appl/chem/gaussian/G03RevB.02/g03/l716.exe) Dipole =-5.39674186D+00 2.07643714D+00-1.81199740D-01 ***** Axes restored to original set ***** Cartesian Forces: Max 0.179041031 RMS 0.030117320 Leave Link 716 at Wed May 12 17:25:08 2004, MaxMem= 65536000 cpu: 0.0 (Enter /mnt/mds/irix65_mips64/appl/chem/gaussian/G03RevB.02/g03/l120.exe) SvSCFP is copying densities from files 528 and 530 to 603. ONIOM: saving gridpoint 2 ONIOM: restoring gridpoint 17 ONIOM: generating point 1 -- low level on model system. Generating MM parameters for model system. I= 16 IAn= 8 Valence=12. JB= 1 J= 14 IAn= 6 IBT=12 Dist= 1.37D+00 Include all MM classes MMInit generated parameter data with length LenPar= 1175. Leave Link 120 at Wed May 12 17:25:14 2004, MaxMem= 65536000 cpu: 3.9 (Enter /mnt/mds/irix65_mips64/appl/chem/gaussian/G03RevB.02/g03/l301.exe) Standard basis: VSTO-3G (5D, 7F) AO basis set in the form of general basis input: 10 0 S 3 1.00 0.000000000000 0.3425250914D+01 0.1543289673D+00 0.6239137298D+00 0.5353281423D+00 0.1688554040D+00 0.4446345422D+00 **** 13 0 SP 3 1.00 0.000000000000 0.2941249355D+01 -0.9996722919D-01 0.1559162750D+00 0.6834830964D+00 0.3995128261D+00 0.6076837186D+00 0.2222899159D+00 0.7001154689D+00 0.3919573931D+00 **** 14 0 SP 3 1.00 0.000000000000 0.2941249355D+01 -0.9996722919D-01 0.1559162750D+00 0.6834830964D+00 0.3995128261D+00 0.6076837186D+00 0.2222899159D+00 0.7001154689D+00 0.3919573931D+00 **** 15 0 SP 3 1.00 0.000000000000 0.5033151319D+01 -0.9996722919D-01 0.1559162750D+00 0.1169596125D+01 0.3995128261D+00 0.6076837186D+00 0.3803889600D+00 0.7001154689D+00 0.3919573931D+00 **** 16 0 SP 3 1.00 0.000000000000 0.5033151319D+01 -0.9996722919D-01 0.1559162750D+00 0.1169596125D+01 0.3995128261D+00 0.6076837186D+00 0.3803889600D+00 0.7001154689D+00 0.3919573931D+00 **** 20 0 S 3 1.00 0.000000000000 0.3425250914D+01 0.1543289673D+00 0.6239137298D+00 0.5353281423D+00 0.1688554040D+00 0.4446345422D+00 **** 21 0 S 3 1.00 0.000000000000 0.3425250914D+01 0.1543289673D+00 0.6239137298D+00 0.5353281423D+00 0.1688554040D+00 0.4446345422D+00 **** The combination of multiplicity 1 and 23 electrons is impossible. Error termination via Lnk1e in /mnt/mds/irix65_mips64/appl/chem/gaussian/G03RevB.02/g03/l301.exe at Wed May 12 17:25:14 2004. Job cpu time: 0 days 0 hours 0 minutes 43.1 seconds. File lengths (MBytes): RWF= 24 Int= 0 D2E= 0 Chk= 7 Scr= 1 real 48.282 user 28.808 sys 14.557 From chemistry-request@ccl.net Wed May 12 12:19:24 2004 Received: from smtp3.es.uci.edu (smtp3.es.uci.edu [128.200.80.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4CHJNkh004069 for ; Wed, 12 May 2004 12:19:24 -0500 Received: from [127.0.0.1] (thlaptop.ps.uci.edu [128.200.11.124]) by smtp3.es.uci.edu (8.12.8/8.12.8) with ESMTP id i4CHLQ5x010002 for ; Wed, 12 May 2004 10:21:29 -0700 Date: Wed, 12 May 2004 10:21:26 -0700 From: Tomoyuki Hayashi To: Subject: Installation Problem of Gaussian 03 with an Opteron Machine Message-Id: <20040512100629.08F0.TOMOYUKH=at=uci.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: Becky! ver. 2.09.01 [ja] X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all, I am trying to install Gaussian 03 (Rev B.04) on an Opteron machine (SuSe9.0 Professional for AMD64). I could not build on that machine, so I copied the binary files build on another machine with ia32p3 (pentium 3) option. But I got an run time error, "l1.exe: bsd/mdutil.c:l607: ntrext1_: Assertion '(lenbuf >=(64 * statbuf.st_blksize))' failed." The binary works fine on a Pentium 4 machine, and the environment ( shell variables, directory structure, set up of pgf77 ) is the same for both machines. Does anyone have the similar problem? Does anyone konw the cause or the solution of this problem ? Tomoyuki, From chemistry-request@ccl.net Tue May 11 20:47:23 2004 Received: from ns.cwp.co.kr ([210.109.76.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4C1lKkh028764 for ; Tue, 11 May 2004 20:47:22 -0500 Received: from insilico ([192.168.203.142]) by ns.cwp.co.kr (8.9.3 (PHNE_25184)/8.9.3) with SMTP id KAA17942 for ; Wed, 12 May 2004 10:45:49 +0900 (KST) Message-ID: <00e001c437c3$618edec0$8ecba8c0@insilico> From: "Sei-Hwan Kim" To: Subject: The pi-pi stacking of hetero-aromatic ring Date: Wed, 12 May 2004 10:49:36 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00DD_01C4380E.D16A9FE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=2.4 required=7.5 tests=HTML_50_60,HTML_MESSAGE, MIME_BASE64_TEXT,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_00DD_01C4380E.D16A9FE0 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 RGVhciBDQ0xlcnMNCg0KSSBhbSBsb29raW5nIGZvciBhIHJlZmVyZW5jZSB0byB0aGUgIHBpLXBp IHN0YWNraW5nIG9mIGhldGVyby1hcm9tYXRpYyByaW5nLiAoIGZhY2UgdG8gZWRnZSwgb2Zmc2V0 LCBmYWNlIHRvIGZhY2UgKSANCg0KUmVnYXJkcw0KDQpTZWFuIA0Kc2VpaGtpbUBjd3AuY28ua3Ig DQo= ------=_NextPart_000_00DD_01C4380E.D16A9FE0 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI4MDAuMTQwMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwv SEVBRD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPg0KPERJVj48 Rk9OVCBzaXplPTI+PEZPTlQgc2l6ZT0zPkRlYXIgQ0NMZXJzPEJSPjxCUj5JIGFtIGxvb2tpbmcg Zm9yIGEgcmVmZXJlbmNlIA0KdG8mbmJzcDt0aGUgJm5ic3A7cGktcGkgc3RhY2tpbmcmbmJzcDtv ZiBoZXRlcm8tYXJvbWF0aWMgcmluZy4gKCBmYWNlIHRvIGVkZ2UsIA0Kb2Zmc2V0LCBmYWNlIHRv IGZhY2UgKSA8L0ZPTlQ+PC9GT05UPjwvRElWPjxGT05UIHNpemU9Mj4NCjxESVY+PEJSPjxGT05U IHNpemU9Mz5SZWdhcmRzPEJSPjxCUj5TZWFuJm5ic3A7PC9GT05UPjwvRElWPg0KPERJVj48QSBo cmVmPSJtYWlsdG86S2ltc2VpaGtpbUBjd3AuY28ua3IiPnNlaWhraW1AY3dwLmNvLmtyPC9BPiA8 L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIHNpemU9Mj48L0ZPTlQ+Jm5ic3A7PC9ESVY+PC9GT05U PjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_00DD_01C4380E.D16A9FE0-- From chemistry-request@ccl.net Tue May 11 17:41:37 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BMfakh022516 for ; Tue, 11 May 2004 17:41:36 -0500 Received: from 128.200.204.233 (dhcp-204233.bio.uci.edu [128.200.204.233]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id i4BMhfux005779 for ; Tue, 11 May 2004 15:43:41 -0700 Date: Tue, 11 May 2004 15:43:35 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <487900017.20040511154335-.at.-uci.edu> To: chemistry-.at.-ccl.net Subject: QM calculate ALA dipeptide at room temperature MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLers, Can I just calculate the frequencies of different conformation of ALA dipeptide at room temperature using G03 to get the free energy surface of phi/psi? Or does anyone know how to get the energy surface of the ALA dipeptide at room temperature? Any suggestion would be helpful. -- Best regards, Qiang Lu mailto:qiangl-.at.-uci.edu From chemistry-request@ccl.net Wed May 12 03:01:57 2004 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4C81tkh010166 for ; Wed, 12 May 2004 03:01:56 -0500 Received: from ptxav (pt-xav.lctn.uhp-nancy.fr [193.50.239.125]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with SMTP id KAA25234; Wed, 12 May 2004 10:05:07 +0200 From: "Xavier ASSFELD" To: "Goedele Roos" , Subject: RE: calculating polarizabilities Date: Wed, 12 May 2004 10:01:47 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) In-Reply-To: <200405111555.RAA26063-.at.-web1.ulb.ac.be> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, certainly the dianion is a closed shell molecule with 1A1 symmetry, and the HOMO is degenerate n times. Hence in the anion, the subset of n orbitals corresponding to the dianion HOMOs are no longer degenerate due to the Hartree-Fock potential and thus the wavefunction does not have the right symmetry and so any properties computed with that wavefunction won't have the right symmetry neither. If this is the case, use a CAS wavefunction or non-integer occupation numbers. Hope this helps. Yours ...Xav Pr. Xavier Assfeld Xavier.Assfeld-.at.-lctn.uhp-nancy.fr Laboratoire de Chimie thiorique (T) 33 3 83 68 43 82 Universiti Henri Poincari (F) 33 3 83 68 43 71 F-54506 Nancy B.P. 239 http://www.lctn.uhp-nancy.fr X> -----Message d'origine----- X> De : Computational Chemistry List [mailto:chemistry-request-.at.-ccl.net]De X> la part de Goedele Roos X> Envoyi : mar. 11 mai 2004 17:56 X> @ : chemistry-.at.-ccl.net X> Objet : CCL:calculating polarizabilities X> X> X> Dear all, X> Calculating the polarizability for a perfect tetrahedral X> dianion, gives for the three diagonal elements of the X> polarizability tensor: (XX)=(YY)=(ZZ). X> But, when I calculate the polarizability of the mono-anion (of X> the same system) on the optimized geometry of the dianion (thus X> on the perfect tetrahedral geometry), the polarizabilitytensor X> gives (XX)=(YY), but the (ZZ) component is different. X> Has anyone also had this problems? X> What can I do to solve this? X> Can anyone give me some advise? X> Thanks in advance for your help, X> Sincerely Yours, X> Goedele Roos X> X> Drs. Goedele Roos X> Dienst Algemene Chemie (ALGC) X> Vrije Universiteit Brussel (VUB) X> Pleinlaan 2 X> B-1050 Brussels X> Tel: 0032-2-629 35 16 X> Fax: 0032-2-629 33 17 X> X> X> X> X> X> -= This is automatically added to each message by the mailing script =- X> To send e-mail to subscribers of CCL put the string CCL: on your X> Subject: line X> and send your message to: CHEMISTRY-.at.-ccl.net X> X> Send your subscription/unsubscription requests to: X> CHEMISTRY-REQUEST-.at.-ccl.net X> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs X> X> If your mail is bouncing from CCL.NET domain send it to the maintainer: X> Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) X> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ X> X> X> X> X> From chemistry-request@ccl.net Wed May 12 07:03:44 2004 Received: from grassmarket.ucs.ed.ac.uk (grassmarket.ucs.ed.ac.uk [129.215.166.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4CC3gkh023531 for ; Wed, 12 May 2004 07:03:42 -0500 Received: from grassmarket.ucs.ed.ac.uk (localhost [127.0.0.1]) by grassmarket.ucs.ed.ac.uk (8.12.10/8.12.10) with ESMTP id i4CC5v1L019638 for ; Wed, 12 May 2004 13:05:57 +0100 (BST) Received: (from nobody@localhost) by grassmarket.ucs.ed.ac.uk (8.12.10/8.12.9/Submit) id i4CC5uRZ019625 for chemistry.-at-.ccl.net; Wed, 12 May 2004 13:05:56 +0100 (BST) X-Authentication-Warning: grassmarket.ucs.ed.ac.uk: nobody set sender to P.Lozano-Casal.-at-.ed.ac.uk using -f Received: from parsons-res11.chem.ed.ac.uk (parsons-res11.chem.ed.ac.uk [129.215.220.249]) by sms.ed.ac.uk (IMP) with HTTP for ; Wed, 12 May 2004 13:05:56 +0100 Message-ID: <1084363556.40a213249c898.-at-.sms.ed.ac.uk> Date: Wed, 12 May 2004 13:05:56 +0100 From: Patricia Lozano-Casal To: chemistry.-at-.ccl.net Subject: Coulombic Potential Summary MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.3 X-Spam-Status: No, hits=0.9 required=7.5 tests=LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, this are the answers that I got to my problem with the Coulombic Potential. Thank you very much for your help. Patricia SUBJECT: QUESTION ABOUT COULOMBIC POTENTIAL Dear all, I am trying to write a program to calculate the electrostatic contribution of the lattice energy for molecular crystals. I have run plane-wave DFT calculations (using the CASTEP package) to calculate the total lattice energy and using Mulliken charges I hoped to estimate the electrostatic contribution by coding a simple Coulombic potential. But, I get really weird results!! I am overestimating my lattice energy by many orders of magnitude. I know that Mulliken charges are not the ideal point charge to use for this but I had not expected my numbers to be that wrong. Could anybody help or if not, could anybody recommend and existing program to use instead (preferably free)? Many thanks, Patricia Lozano-Casal (p.lozano-casal.-at-.ed.ac.uk) -------------------------------------------------------------------- Calculating electrostatic potentials of crystals can be a very daunting task considering that the sum of Coulombic interactions in an infinite crystal is only conditionally convergent. That is it only converges (when it actually does converge) to a finite number because of the alternating signs of the terms in the series. As a result the summation can have serious problems with numerical error. So, I hope you are using an Ewald method to calculate the electrostatic contribution and that your Muliken charges in your unit cell sum to exactly zero. To the first point, the Ewald sum is THE way to calculate the electrostatic energy of an infinite lattice, but even with it care must be taken to reduce round-off error in the numerical calculation. To the second point, if your unit cell is not neutral, then the strict sum includes the summation of an infinite number of positive interactions, which of course is an infinite value. In a truncated (i.e. any real numerical) Ewald summation, this could just lead to a large finite value such as you are getting. Just a thought. Malcolm ------------------------------------------------------------- Dear Patricia, GULP (General Utility Lattice Code), written by Julian Gale, can calculate very easily the electrostatic contribution to the lattice energy of a crystal. You should specify the charges in the input file, although some methods to estimate them (e.g. by electronegativity equalisation) are also implemented. The code is free for academic users. Best regards, Ricardo. -- Room 85, School of Chemistry, Joseph Black Building, Kings Buildings, West Mains Road, Edinburgh, EH9 3JJ United Kingdom Tel: +441316504804 From chemistry-request@ccl.net Wed May 12 13:37:47 2004 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4CIbkkh008474 for ; Wed, 12 May 2004 13:37:46 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout4.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i4CIdvAe006383; Wed, 12 May 2004 11:40:01 -0700 Received: from u.washington.edu (D-128-95-235-217.dhcp4.washington.edu [128.95.235.217]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i4CIdvOk009637 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Wed, 12 May 2004 11:39:57 -0700 Message-ID: <40A26F7F.1090101:at:u.washington.edu> Date: Wed, 12 May 2004 11:39:59 -0700 From: Oliver Hucke Reply-To: ohucke:at:u.washington.edu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Sei-Hwan Kim , CCL Subject: Re: CCL:The pi-pi stacking of hetero-aromatic ring References: <00e001c437c3$618edec0$8ecba8c0@insilico> Content-Type: text/plain; charset=x-windows-949 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Sean, this is a reference to a very nice recent review: @Article{60038, author = {E. A. Meyer and R. K. Castellano and F. Diederich}, title = {Ineractions with aromatic rings in chemical and biological recognition}, journal = {Angw. Chem. Int. Ed.}, year = {2003}, key = {protein structure ; aromatic interactions ; review}, volume = {42}, pages = {1210-1250}, } Best, Oliver Sei-Hwan Kim wrote: > Dear CCLers > > I am looking for a reference to the pi-pi stacking of hetero-aromatic > ring. ( face to edge, offset, face to face ) > > Regards > > Sean > seihkim:at:cwp.co.kr > -- _______________________________________________________________ Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke:at:u.washington.edu _______________________________________________________________