From chemistry-request@ccl.net Mon Aug 9 07:45:46 2004 Received: from mxsf30.cluster1.charter.net (mxsf30.cluster1.charter.net [209.225.28.230]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i79CjiQN017793 for ; Mon, 9 Aug 2004 07:45:44 -0500 Received: from mxip17.cluster1.charter.net (mxip17a.cluster1.charter.net [209.225.28.147]) by mxsf30.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id i79CrO0S006759 for ; Mon, 9 Aug 2004 08:53:29 -0400 Received: from 24.247.172.122.bay.mi.chartermi.net (HELO mmserver) (24.247.172.122) by mxip17.cluster1.charter.net with ESMTP; 09 Aug 2004 08:53:25 -0400 Message-Id: <3a57rt$5cdvvh^at^mxip17a.cluster1.charter.net> X-Ironport-AV: i="3.83,114,1089000000"; d="scan'208"; a="180813809:sNHT13421224" From: "Jim Kress" To: Subject: MCCI in GAMESS Date: Mon, 9 Aug 2004 08:53:15 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 Thread-Index: AcR8hf9d8PXi/+j+Rz6x0ml3/38WyQBiblgw X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 In-Reply-To: X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net What is the meaning of the statement: -MCCI- BASED ON OPTIMIZED ORBITALS In the context of doing a state averaged MCSCF calculation with GAMESS? Thanks. Jim From chemistry-request@ccl.net Mon Aug 9 07:22:29 2004 Received: from web15407.mail.cnb.yahoo.com (web15407.mail.cnb.yahoo.com [202.43.216.210]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i79CMLQN016036 for ; Mon, 9 Aug 2004 07:22:22 -0500 Message-ID: <20040809123006.22102.qmail..at..web15407.mail.cnb.yahoo.com> Received: from [162.105.5.116] by web15407.mail.cnb.yahoo.com via HTTP; Mon, 09 Aug 2004 20:30:06 CST Date: Mon, 9 Aug 2004 20:30:06 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: value of MIF from GRID ver. 22 To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.5 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 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, I have used GRID ver. 22 to calculate the MIF. I found that many of the values given by *.kont is ZERO for certain grid. I don't know if I should discard those value when I try to analysis the MIF using a third-party statistic software. Would anyone here like to give me some information about the range of the value of MIF? Any suggestions and/or comments will be really appreciated. Thanks in advance! Best wishes, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong..at..yahoo.com.cn _________________________________________________________ Do You Yahoo!? 150MrGzMP37h?qKQ#,4xDz43HkRt@V5nLC http://music.yisou.com/ C..at..E.CwPGS&SP>!SP#,KQ1iC@MMJG1000UW#,QE;"5gSJWTVz@)H]#! http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/event/mail_1g/ From chemistry-request@ccl.net Sun Aug 8 19:03:37 2004 Received: from relay4.delfa.net (relay4.delfa.net [193.125.210.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7903ZO8006250 for ; Sun, 8 Aug 2004 19:03:36 -0500 X-Envelope-To: Received: from sycorax.delfa.net (relay4.delfa.net [193.125.210.9]) by sycorax.delfa.net (8.13.0/8.13.0/Sycorax.Delfa) with ESMTP id i790BIfN003687 for ; Mon, 9 Aug 2004 04:11:18 +0400 Received: (from uucp@localhost) by sycorax.delfa.net (8.13.0/8.12.9/Submit) with UUCP id i790BIoC003686 for chemistry..at..ccl.net; Mon, 9 Aug 2004 04:11:18 +0400 Received: from goblin ([192.168.5.1] helo=xenon.spb.ru ident=dima) by shadow with esmtp (Exim 3.35 #1 (Debian)) id 1BtxeJ-0000kg-00; Mon, 09 Aug 2004 04:04:23 +0400 Message-ID: <4116BF87.5070407..at..xenon.spb.ru> Date: Mon, 09 Aug 2004 04:04:23 +0400 From: Dmitry Rozmanov User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040528 Debian/1.6-7 X-Accept-Language: ru, en MIME-Version: 1.0 To: Frank Jensen , CCL Subject: Re: [Gamess] incorrect curvature with EFRAG optimization References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.4 required=7.5 tests=MY_BAD_DOT,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Frank, Thank you for the suggestion. I've written a python script which automatically restarts the calculation if one fails. Much better now ;). I put KDIAG=2 in the template and next time it fails the modified input will go to work. I will inform you immediately as it is clear. Up to now the longest run has been 179 steps and the shortest one -- just only 2. Should I try both 2 and 3? I have checked INPUT.DOC and the description is not too clear. And about the routine. So it is bugged then, isn't it? Will you tell Mike about this? Could it be fixed in the next release of GAMESS? Thank you for your help. Best regards. ---Dmitry. Frank Jensen wrote: > Dmitry, > I took a look at your smallest test cases, > and could reproduce the error within two steps when I used > the STO-3G basis, although with the june 20 2002 version > of gamess. At least for this specific case, the > problem is that the diagonalization routine for getting > the hessian eigenvalues fails, and gives NaN for several > of the eigenvalues. The optimization routine seems to > work fine. The easy work-around is to use another > diagonalization routine, by setting the KDIAG in $SYSTEM > to either 2 or 3. Could you try this and see if it solves your > problems? Let me know in either case. > Frank > > > On Sat, 7 Aug 2004, Dmitry Rozmanov wrote: > From chemistry-request@ccl.net Mon Aug 9 09:25:20 2004 Received: from hellmouth4.gatech.edu (hellmouth4.gatech.edu [130.207.165.164]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i79EPJQN026813 for ; Mon, 9 Aug 2004 09:25:19 -0500 Received: from hellmouth4.gatech.edu (localhost [127.0.0.1]) by hellmouth4.gatech.edu (Postfix) with SMTP id D14ABA56B for ; Mon, 9 Aug 2004 10:33:05 -0400 (EDT) (envelope-from ok16)at(mail.gatech.edu) Received: from acmez.gatech.edu (acmez.prism.gatech.edu [130.207.171.28]) by hellmouth4.gatech.edu (Postfix) with ESMTP id BD84BA54B for ; Mon, 9 Aug 2004 10:33:05 -0400 (EDT) (envelope-from ok16)at(mail.gatech.edu) Received: by acmez.gatech.edu (Postfix, from userid 11564) id 957A84ECB0; Mon, 9 Aug 2004 10:33:05 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by acmez.gatech.edu (Postfix) with ESMTP id 78F274FE87 for ; Mon, 9 Aug 2004 10:33:05 -0400 (EDT) (envelope-from ok16)at(mail.gatech.edu) Date: Mon, 9 Aug 2004 10:33:05 -0400 (EDT) From: Ohyun Kwon X-X-Sender: Reply-To: Tommy Ohyun Kwon To: Subject: stability of radicals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS 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 CCLers' I would like to know what is the best way to evaluate the stability of radical cation and anion. Thank you very much for your kind advices in advance. Have a good day! Yours, Tommy Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon)at(chemistry.gatech.edu From chemistry-request@ccl.net Mon Aug 9 10:03:54 2004 Received: from Post-Office.UH.EDU (LISTSERV.UH.EDU [129.7.1.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i79F3rQN029989 for ; Mon, 9 Aug 2004 10:03:53 -0500 Received: from nyssa.bchs.uh.edu (Nyssa.BCHS.uh.edu [129.7.238.204]) by Post-Office.UH.EDU (PMDF V6.0-025 #30827) with ESMTP id <0I2604D35Q71UM!at!Post-Office.UH.EDU> for chemistry!at!ccl.net; Mon, 09 Aug 2004 10:11:25 -0500 (CDT) Date: Mon, 09 Aug 2004 09:05:44 -0500 From: Jerry Ebalunode Subject: Re: CCL:Parallel Jaguar on x86-64 / MPI question In-reply-to: <41139F8C.3040405!at!pobox.com> To: Eric Bennett Cc: "'chemistry!at!ccl.net'" Reply-to: jebalunode!at!uh.edu Message-id: <200408091005.45366.jebalunode!at!uh.edu> Organization: University of Houston MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.6.2 References: <41139F8C.3040405!at!pobox.com> X-Spam-Status: No, hits=0.3 required=7.5 tests=FCS_URI_NODOTS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net It seems you are requesting two processors for your job but your mpi configuration only reports one as being available. If you are using mpich, you could add the following option to your mpirun argument mpirun -np N -machinefile my_machinefile ./program N = no. of processors (in yourcase 2) my_machinefile = machinefile list e.g. pobox.com:2 Two in here means that server (pobox.com) has two processors Hope this helps. On Friday 06 August 2004 11:11 am, Eric Bennett wrote: > Hello, > > I have seen people report running Jaguar succesfully on x86_64 systems, > but I have not seen any reports as to whether these were parallel or > serial jobs. I am having trouble running parallel jobs on an SMP Intel > x86_64 system. I assume that because I'm an MPI novice, my problem is a > configuration error, but Schrodinger's first response was to say that > they do not compile for 64-bit systems. > > So, has anyone run parallel Jaguar on x86_64 succesfully? My serial > jobs work fine. > > Alternatively, can someone who knows more about MPI than I do suggest > where I might have gone wrong to obtain the following error, assuming > that it is not an incompatibility with x86_64? The mpich test suite > appears to run fine and uses all the CPUs. > > > FATAL: FATAL: MPI_Comm_size (2) does not equal nprocs (1)MPI_Comm_size > (2) does not equal nprocs (1)[0] MPI Abort by user Aborting program ! > [1] MPI Abort by user Aborting program ! > [0] Aborting program! > [1] Aborting program! > p0_27431: p4_error: : 1 > p1_27432: p4_error: : 1 > > > More info: > > Jaguar version 5.5, release 16 > > [bennette@localhost bms]$ uname -a > Linux localhost.localdomain 2.4.21-15.EL #1 SMP Thu Apr 22 00:09:47 EDT > 2004 x86_64 x86_64 x86_64 GNU/Linux > > > TIA, > Eric -- Jerry Ebalunode Ph.D. Candidate (Advisor: Asoc. Professor Jim Briggs Ph.D.) RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston 4800 Calhoun Road Houston, TX 77204 From chemistry-request@ccl.net Mon Aug 9 09:22:51 2004 Received: from hellmouth5.gatech.edu (hellmouth5.gatech.edu [130.207.165.165]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i79EMpQN026587 for >ccl.net>; Mon, 9 Aug 2004 09:22:51 -0500 Received: from hellmouth5.gatech.edu (localhost [127.0.0.1]) by hellmouth5.gatech.edu (Postfix) with SMTP id 448A51D1D33 for >ccl.net>; Mon, 9 Aug 2004 10:30:35 -0400 (EDT) (envelope-from ok16<>mail.gatech.edu) Received: from acmez.gatech.edu (acmez.prism.gatech.edu [130.207.171.28]) by hellmouth5.gatech.edu (Postfix) with ESMTP id B798E1D1E00 for >ccl.net>; Mon, 9 Aug 2004 10:30:13 -0400 (EDT) (envelope-from ok16<>mail.gatech.edu) Received: by acmez.gatech.edu (Postfix, from userid 11564) id 6A1924ECB0; Mon, 9 Aug 2004 10:30:13 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by acmez.gatech.edu (Postfix) with ESMTP id 4C1964FE87 for >ccl.net>; Mon, 9 Aug 2004 10:30:13 -0400 (EDT) (envelope-from ok16<>mail.gatech.edu) Date: Mon, 9 Aug 2004 10:30:13 -0400 (EDT) From: Ohyun Kwon >mail.gatech.edu> X-X-Sender: >acmez.gatech.edu> Reply-To: Tommy Ohyun Kwon >chemistry.gatech.edu> To: >ccl.net> Subject: unit of electrostatic potential Message-ID: >acmez.gatech.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS 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 CClers' I have created electrostatic potential maps using the cube-generator in Gaussian. I would like to know what units the resulting potential is in either eV or kcal/mol. I would greatly appreciate it if you would kindly give me an answer to that. Thank you very much for your kind attention all the time. Have a good day! Best wishes, Tommy Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon<>chemistry.gatech.edu From chemistry-request@ccl.net Mon Aug 9 10:58:04 2004 Received: from mail2.zrz.tu-berlin.de (mail2.zrz.TU-Berlin.DE [130.149.4.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i79Fw3QN032521 for ; Mon, 9 Aug 2004 10:58:03 -0500 Received: from localhost ([127.0.0.1] helo=mail2.zrz.TU-Berlin.DE) by mail2.zrz.tu-berlin.de with esmtp (exim-4.41) id 1BuCej-0002Vh-AA; Mon, 09 Aug 2004 18:05:49 +0200 Received: from mail2.zrz.TU-Berlin.DE ([130.149.4.14]) by mail2.zrz.TU-Berlin.DE (MailMonitor for SMTP v1.2.2 ) ; Mon, 9 Aug 2004 18:05:48 +0200 (CEST) Received: from mailbox.tu-berlin.de ([130.149.4.18]) by mail2.zrz.tu-berlin.de with esmtp (exim-4.41) id 1BuCei-0002VO-CK; Mon, 09 Aug 2004 18:05:48 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailbox.tu-berlin.de with esmtp (exim-4.41) id 1BuCei-0004S5-N8; Mon, 09 Aug 2004 18:05:48 +0200 Mime-Version: 1.0 X-Sender: chwu0531=at=mailbox.zrz.tu-berlin.de Message-Id: In-Reply-To: <20040806135443.6383.qmail=at=web52005.mail.yahoo.com> References: <20040806135443.6383.qmail=at=web52005.mail.yahoo.com> Date: Mon, 9 Aug 2004 18:05:47 +0200 To: Konstantin Kudin From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:SCF Convergence problem in G03 Cc: chemistry=at=ccl.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" X-Virus-Scanned: Sophos MailMonitor on mail2.zrz.tu-berlin.de; Mon, 09 Aug 2004 18:05:48 +0200 X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_BAD_DOT,NO_RDNS2, RM_ft_Iso8859 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 i79Fw4QN032525 > > First, look at the initial gues around the homo-lumo gap.. Are there >> unfilled orbitals that are essentially degenerate with orbitals to be >> filled? If so a single determinate solution may not work.... and bad >> convergence would not be a surprise > > Actually, does anyone know examples where B3LYP only leads to >solutions where LUMO is below HOMO in energy, i.e. with holes below the >Fermi level? My impression was that 20% of the HF exchange pretty much >always stabilized the occupied orbitals, in the same way as the HF >method does. > ... look for lanthanide compounds, where partially filled 4f levels should be below doubly occupied ligand orbitals. -- +---------------------------------+----------------------------------+ | Prof. Christoph van W|llen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitdt Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Stra_e des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen=at=TU-Berlin.De | +---------------------------------+----------------------------------+ From chemistry-request@ccl.net Mon Aug 9 08:35:22 2004 Received: from post.it.helsinki.fi (post.it.helsinki.fi [128.214.205.132]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i79DZKQN022485 for ; Mon, 9 Aug 2004 08:35:21 -0500 Received: from soul.it.helsinki.fi (soul.it.helsinki.fi [128.214.189.108]) by post.it.helsinki.fi (8.12.11/8.12.11) with ESMTP id i79Dh33G006883 for ; Mon, 9 Aug 2004 16:43:05 +0300 (EEST) Received: from soul.it.helsinki.fi (localhost [127.0.0.1]) by soul.it.helsinki.fi (8.12.10/8.12.10) with ESMTP id i79Dh3x3196994 for ; Mon, 9 Aug 2004 16:43:03 +0300 (EEST) Received: from localhost (mpjohans@localhost) by soul.it.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id i79Dh32C196998 for ; Mon, 9 Aug 2004 16:43:03 +0300 (EEST) X-Authentication-Warning: soul.it.helsinki.fi: mpjohans owned process doing -bs Date: Mon, 9 Aug 2004 16:43:03 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans=at=soul.it.helsinki.fi To: chemistry=at=ccl.net Subject: CCL:Winter School in Theoretical Chemistry 2004 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id i79DZMQN022494 Hello All! The already traditional Winter School in Theoretical Chemistry will take place in December, the week of Monday 13th to Friday 17th, 2004. Venue: University of Helsinki, Finland Topic: A Frontier of Chemistry: New Species Level: Post-graduate and research, for scientists already involved in computational quantum chemistry Speakers at this year's School include: Lester Andrews Karl Christe Margaret-Jane Crawford Laura Gagliardi Michael C. L. Gerry Martin Head-Gordon Thomas M. Klapvtke Markku Rdsdnen Konrad Seppelt Lai-Sheng Wang Vivian Wing-Wah Yam The School is free of charge for academics, but registration is required. The registration dead-line is November 15th. Attendance is limited by space restrictions imposed by the lecture hall. This year, attendees are encouraged to submit a poster abstract; a proper poster session is now part of the School! For more info, have a look at the web page of the School: http://www.chem.helsinki.fi/Info/WinterSchool/ws2004.html See you in Helsinki in December, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson=at=helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50185 FAX : +358-9-191 50169 From chemistry-request@ccl.net Mon Aug 9 17:57:13 2004 Received: from web52404.mail.yahoo.com (web52404.mail.yahoo.com [206.190.39.112]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i79MvC51013961 for >ccl.net>; Mon, 9 Aug 2004 17:57:12 -0500 Message-ID: <20040809211840.99966.qmail<>web52404.mail.yahoo.com> Received: from [192.26.250.234] by web52404.mail.yahoo.com via HTTP; Mon, 09 Aug 2004 14:18:40 PDT Date: Mon, 9 Aug 2004 14:18:40 -0700 (PDT) From: Eric Hu >yahoo.com> Subject: summary: peptide conformational search To: chemistry >ccl.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Here are the two answers I got. Thank Dirk and Jeff again. A co-worker made his PhD-Thesis on conformational analysis of (cyclic) peptids, but its in German: http://diss.ub.uni-duesseldorf.de/ebib/diss/show?dissid=150 Regards, Dirk. A 21 residue peptide would not be tractable to a systematic search. Monte Carlo and/or high-temperature molecular dynamics are your best bets. To get started with some ideas, you may want to take a look at the following: 1. Prabhu NV, Siddiqui SA, McMurray JS, Pettitt BM. 2001. Structural basis for the activity of pp60c-src protein tyrosine kinase inhibitors. Biopolymers 59: 167 2. Levy Y, Becker OM. 2001. Energy landscapes of conformationally constrained peptides. J. Chem. Phys. 114: 993 3. Worth GA, Nardi F, Wade RC. 1998. Use of multiple molecular dynamics trajectories to study biomolecules in solution: The YTGP peptide. J Phys Chem B 102: 6260 There are many other examples in the literature. Jeff __________________________________ Do you Yahoo!? Yahoo! Mail - 50x more storage than other providers! http://promotions.yahoo.com/new_mail