From chemistry-request@server.ccl.net Thu Nov 11 07:39:03 1999 Received: from mtu.ru (ns.mtu.ru [195.34.32.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA30401 for ; Thu, 11 Nov 1999 07:39:02 -0500 Received: from dial52009.mtu-net.ru (dial52009.mtu-net.ru [195.34.52.9]) by mtu.ru (Postfix) with SMTP id AD65B2CDB for ; Thu, 11 Nov 1999 15:31:28 +0300 (MSK) Received: by dial52009.mtu-net.ru with Microsoft Mail id <01BF2C59.D144C600@dial52009.mtu-net.ru>; Thu, 11 Nov 1999 15:31:26 +0300 Message-ID: <01BF2C59.D144C600@dial52009.mtu-net.ru> From: "M.D." To: "'Computational Chemistry List'" Subject: Transition metal complexes Date: Thu, 11 Nov 1999 12:13:41 +0300 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Recipient: chemistry@ccl.net Dear CCLers, I would be grateful for any reference to recent reviews about applications of ab-initio and/or semiempirical methods to transition metal complexes (especially for the first row metals), Best regards, Mike. From chemistry-request@server.ccl.net Thu Nov 11 08:19:20 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA30594 for ; Thu, 11 Nov 1999 08:18:47 -0500 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @mailout.lrz-muenchen.de:chemistry@ccl.net; Thu, 11 Nov 1999 14:11:14 +0100 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id QAA07397; Fri, 5 Nov 1999 16:16:54 +0100 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <3822F4E5.6BB702EA@physik.tu-muenchen.de> Date: Fri, 05 Nov 1999 16:16:53 +0100 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: AIM Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I tried to calculate the atomic charges of a molecular cluster with Gaussian and the AIM keyword but everytime the job crashed with the following message: ********************************************************************** Properties of atoms in molecules using the SCF density. ********************************************************************** I. ATTRACTORS ------------------------------------------------------------------------------- Attr. Cartesian Coordinates Nucleus Density X Y Z (Distance) Total Spin ------------------------------------------------------------------------------- 1 -4.501426 1.747284 0.000000 C (0.000001) 0.12085E+03 0.00000E+00 2 -2.080224 2.776501 0.000000 C (0.000001) 0.12083E+03 0.00000E+00 3 0.000000 1.197788 0.000000 C (0.000001) 0.12087E+03 0.00000E+00 4 -0.341103 -1.445053 0.000000 C (0.000003) 0.12073E+03 0.00000E+00 5 -2.802324 -2.443379 0.000000 C (0.000001) 0.12087E+03 0.00000E+00 6 -4.874570 -0.858433 0.000000 C (0.000001) 0.12083E+03 0.00000E+00 7 -3.017814 -4.411312 0.000000 H (0.062232) 0.39223E+00 0.00000E+00 8 -6.710564 -1.601924 0.000000 H (0.061768) 0.39106E+00 0.00000E+00 9 -6.074421 2.956412 0.000000 H (0.061717) 0.39201E+00 0.00000E+00 10 -1.836507 4.742091 0.000000 H (0.062146) 0.39028E+00 0.00000E+00 11 1.826025 1.950535 0.000000 H (0.066294) 0.38512E+00 0.00000E+00 12 1.764594 -3.188295 0.000000 C (0.000002) 0.12105E+03 0.00000E+00 13 4.110660 -2.591313 0.000000 N (0.000008) 0.19680E+03 0.00000E+00 14 6.231743 2.899177 0.000000 O (0.000007) 0.29713E+03 0.00000E+00 15 6.306280 1.224053 0.000000 H (0.118258) 0.37924E+00 0.00000E+00 16 7.827037 3.407977 0.000000 H (0.111428) 0.39136E+00 0.00000E+00 FATAL ERROR: DUPLICATE CRITICAL POINTS FOUND: 16 13 Error termination via Lnk1e in /usr/local/gaussian94/g94/l609.exe. Does anyone know how to fix this problem? Thanks Thomas Mehnert PS.: Here is the command section of the input stream: #P CIS(Root=1,NStates=1,Singlets,Direct,TransitionDensities)/cc-pVDZ Test SCF=(Direct,VarAcc,Tight,TightLinEq) Symmetry=(Int,Grad,SCF) IOP(2/16=2) GFInput AIM=Charges From chemistry-request@server.ccl.net Thu Nov 11 10:27:06 1999 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA31442 for ; Thu, 11 Nov 1999 10:27:06 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with SMTP id KAA14847; Thu, 11 Nov 1999 10:19:20 -0500 (EST) Date: Thu, 11 Nov 1999 10:19:20 -0500 (EST) From: "C.F. Matta" To: Mehnert Thomas cc: chemistry@ccl.net Subject: Re: CCL:AIM In-Reply-To: <3822F4E5.6BB702EA@physik.tu-muenchen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Mehnert, Try Bader's free software package: AIMPAC at http://www.chemistry.mcmaster.ca/aimpac/ Itis very stable. Cheers, Cherif ....................................................................... Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ....................................................................... On Fri, 5 Nov 1999, Mehnert Thomas wrote: > I tried to calculate the atomic charges of a molecular cluster with > Gaussian and the AIM keyword but everytime the job crashed with the > following message: > > ********************************************************************** > > Properties of atoms in molecules using the SCF density. > > ********************************************************************** > > > I. ATTRACTORS > > ------------------------------------------------------------------------------- > > Attr. Cartesian Coordinates Nucleus Density > X Y Z (Distance) Total > Spin > ------------------------------------------------------------------------------- > > 1 -4.501426 1.747284 0.000000 C (0.000001) 0.12085E+03 > 0.00000E+00 > 2 -2.080224 2.776501 0.000000 C (0.000001) 0.12083E+03 > 0.00000E+00 > 3 0.000000 1.197788 0.000000 C (0.000001) 0.12087E+03 > 0.00000E+00 > 4 -0.341103 -1.445053 0.000000 C (0.000003) 0.12073E+03 > 0.00000E+00 > 5 -2.802324 -2.443379 0.000000 C (0.000001) 0.12087E+03 > 0.00000E+00 > 6 -4.874570 -0.858433 0.000000 C (0.000001) 0.12083E+03 > 0.00000E+00 > 7 -3.017814 -4.411312 0.000000 H (0.062232) 0.39223E+00 > 0.00000E+00 > 8 -6.710564 -1.601924 0.000000 H (0.061768) 0.39106E+00 > 0.00000E+00 > 9 -6.074421 2.956412 0.000000 H (0.061717) 0.39201E+00 > 0.00000E+00 > 10 -1.836507 4.742091 0.000000 H (0.062146) 0.39028E+00 > 0.00000E+00 > 11 1.826025 1.950535 0.000000 H (0.066294) 0.38512E+00 > 0.00000E+00 > 12 1.764594 -3.188295 0.000000 C (0.000002) 0.12105E+03 > 0.00000E+00 > 13 4.110660 -2.591313 0.000000 N (0.000008) 0.19680E+03 > 0.00000E+00 > 14 6.231743 2.899177 0.000000 O (0.000007) 0.29713E+03 > 0.00000E+00 > 15 6.306280 1.224053 0.000000 H (0.118258) 0.37924E+00 > 0.00000E+00 > 16 7.827037 3.407977 0.000000 H (0.111428) 0.39136E+00 > 0.00000E+00 > > FATAL ERROR: DUPLICATE CRITICAL POINTS FOUND: 16 13 > Error termination via Lnk1e in /usr/local/gaussian94/g94/l609.exe. > > > > Does anyone know how to fix this problem? > > Thanks > > Thomas Mehnert > > > PS.: Here is the command section of the input stream: > #P CIS(Root=1,NStates=1,Singlets,Direct,TransitionDensities)/cc-pVDZ > Test > SCF=(Direct,VarAcc,Tight,TightLinEq) Symmetry=(Int,Grad,SCF) IOP(2/16=2) > GFInput AIM=Charges > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Nov 11 13:04:03 1999 Received: from panix3.panix.com (9mk3SCv3l2uOcSJx8u5xJMp12HWvMyQ7@panix3.panix.com [166.84.0.228]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA32130 for ; Thu, 11 Nov 1999 13:04:02 -0500 From: kynn@panix.com Received: (from kynn@localhost) by panix3.panix.com (8.8.5/8.8.8/PanixU1.4) id MAA24019; Thu, 11 Nov 1999 12:56:26 -0500 (EST) Date: Thu, 11 Nov 1999 12:56:26 -0500 (EST) Message-Id: <199911111756.MAA24019@panix3.panix.com> To: CHEMISTRY@ccl.net Subject: Umbrella sampling: where are the technical details? Hi! I'm gearing up to do several umbrella sampling studies using a simple ("minimalist") model of protein-like folding. I've never done this sort of thing, and though I understand the theory behind it well enough, but it would save me a lot of trial-and-error to read a technical review of umbrella sampling addressing technical details like the choice of parameters such as bin width(s), temperatures, and relative strength of the various coupling constants for the restraining potentials (I need at least two reaction coordinates, with corresponding restraining potentials; I'll use a histogramming technique to combine data produced at different temperatures). A review that also addressed issues specific to the study of protein-like folding would be ideal, but this is perhaps too much to ask. Anyway, if anyone knows of such a review, please let me know of it. I'll post a summary of responses. Thanks! Kynn Jones From chemistry-request@server.ccl.net Thu Nov 11 15:49:09 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA32756 for ; Thu, 11 Nov 1999 15:49:08 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id OAA09786 for ; Thu, 11 Nov 1999 14:41:31 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.1b+Sun/8.9.1) with ESMTP id OAA00932 for ; Thu, 11 Nov 1999 14:41:31 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Thu, 11 Nov 1999 14:41:31 -0600 (CST) From: Jim Phillips To: chemistry@server.ccl.net Subject: ANNOUNCE: NAMD 2.1 Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +--------------------------------------------------------------------+ | | | NAMD 2.1 Release Announcement | | | +--------------------------------------------------------------------+ November 11, 1999 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.1 is more stable than NAMD 2.0 and adds several new features: - Tcl scripting language interface and config file parsing. - Mollified impulse multiple timestepping method. - Faster particle mesh Ewald implementation. - Periodic boundaries for non-orthogonal cells. - New interactive molecular dynamics interface to VMD. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Thu Nov 11 18:33:29 1999 Received: from chem.boisestate.edu (chem10.idbsu.edu [132.178.136.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA00707 for ; Thu, 11 Nov 1999 18:33:28 -0500 Received: from labasst (LABASST.boisestate.edu [132.178.213.224]) by chem.boisestate.edu (8.8.5/8.8.5) with SMTP id QAA06743 for ; Thu, 11 Nov 1999 16:34:07 -0700 Message-Id: <3.0.6.32.19991111162611.009257e0@chem.boisestate.edu> X-Sender: bmoritz@chem.boisestate.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 11 Nov 1999 16:26:11 -0700 To: chemistry@ccl.net From: Benny Moritz Subject: Chkpt File Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Netters, How do I read a checkpoint file? I have been unable to read my checkpoint files in GaussView (G98). I have been using an FTP program (CuteFTP) and all my gaussian jobs are stored in one directory, so I decided to make sub-directories to sort out all my jobs. I transferred the files from the FTP to my personal computer and then back into their appropriate sub-directories using ASCII mode for both transfers. But when I go into GaussView to view my checkpoint file an error message comes up saying unable to read checkpoint file. Is there anyway to fix my problem, or am I screwed? Thank You, Ben Moritz "Whom the Gods destroy, they first make mad."