From chemistry-request@server.ccl.net Sat Nov 27 11:36:59 1999 Received: from yeager5.chem.tamu.edu (yeager5.chem.tamu.edu [165.91.176.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA18813 for ; Sat, 27 Nov 1999 11:36:58 -0500 Received: (from noj@localhost) by yeager5.chem.tamu.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) id QAA28030; Sat, 27 Nov 1999 16:30:54 +0100 (MET) Date: Sat, 27 Nov 1999 16:30:54 +0100 (MET) Message-Id: <199911271530.QAA28030@yeager5.chem.tamu.edu> From: noj malcolm To: basiuk@nuclecu.unam.mx CC: chemistry@ccl.net In-reply-to: (message from Vladimir Basiuk on Fri, 26 Nov 1999 13:26:49 -0600 (CST)) Subject: Re: CCL:TS Validmir, I think I would add another necessary criteria to the comments by Prof. Lewers- that to be at a TS the gradients of the energy are zero w.r.t nuclear displacement. In other words you need to be at a stationary point, which has only one -ve frequency. noj -------------------------------------------------------------------------- Dr. N.O.J. Malcolm e-mail:malcolm@mail.chem.tamu.edu Department of Chemistry Texas A&M University College Station TX 77845 U.S.A -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Nov 26 16:54:01 1999 Received: from msx.delphi.com (msx.delphi.com [199.93.4.215]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13560 for ; Fri, 26 Nov 1999 16:54:00 -0500 Received: from lrz.uni-muenchen.de (lsajca1-ar3-012-122.biz.dsl.gtei.net [4.3.12.122]) by msx.delphi.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0) id XRH15A5J; Fri, 26 Nov 1999 15:54:00 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id NAA18302; Fri, 26 Nov 1999 13:45:07 -0800 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14398.65378.773479.640825@lrz.uni-muenchen.de> Date: Fri, 26 Nov 1999 13:45:06 -0800 (PST) To: antonio luiz oliveira de noronha Cc: chemistry@ccl.net, Subject: CCL:BeoWolf In-Reply-To: References: X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid antonio luiz oliveira de noronha writes: > CCL friends > Where may I find information about how to build a beowolf cluster, his > capabilities and other information?? > Best regards A very good site is The Beowulf Underground: http://www.beowulf-underground.org/ There is an excellent book on the topic as well: http://mitpress.mit.edu/book-home.tcl?isbn=026269218X From chemistry-request@server.ccl.net Fri Nov 26 19:53:24 1999 Received: from europe.std.com (europe.std.com [199.172.62.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA14400 for ; Fri, 26 Nov 1999 19:53:24 -0500 Received: from world.std.com (root@world-f.std.com [199.172.62.5]) by europe.std.com (8.9.3/8.9.3) with ESMTP id SAA07174 for ; Fri, 26 Nov 1999 18:47:39 -0500 (EST) Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id SAA15572 for chemistry@ccl.net; Fri, 26 Nov 1999 18:46:48 -0500 (EST) Date: Fri, 26 Nov 1999 18:46:48 -0500 (EST) From: Joe M Leonard Message-Id: <199911262346.SAA15572@world.std.com> To: chemistry@ccl.net Subject: Monte Carlo question Folks, I'm at home without notes, tinkering with some code... Does any reader know the proper conversion factor(s) for doing MC work with energies in KCal/mol? I would greatly appreciate learning what I've got to stick in my code to work this in - or pointers to examples I can find to educate me on this. Email me directly, or to CCL if you'd like... Thanks in advance! Joe Leonard jle@world.std.com P.S. One of the bad things of Linux boxen :-)... From chemistry-request@server.ccl.net Sat Nov 27 03:50:33 1999 Received: from mb04.swip.net (mb04.swip.net [193.12.122.208]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA16148 for ; Sat, 27 Nov 1999 03:50:33 -0500 Received: from [212.151.98.32] (d212-151-98-32.swipnet.se [212.151.98.32]) by mb04.swip.net (8.8.8/8.8.8) with ESMTP id IAA17536 for ; Sat, 27 Nov 1999 08:44:12 +0100 (MET) X-Sender: peo@compchem.dfh.dk Message-Id: In-Reply-To: <383EFD6E.7188@trentu.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 27 Nov 1999 08:45:13 +0100 To: chemistry@ccl.net From: Per-Ola Norrby Subject: Re: CCL:TRANSITION STATE AND IMAGINARY..., ANSWER >Hello, Vladimir Basiuk asked: >Dear CCLers, > >Please could you help me to clarify the following point. >Is the presence of one imaginary frequency the necessary and sufficient >criterion to consider the structure as TS? >Thank you and best regards, >Vladimir > *** > >The answer is yes. A structure is a TS if and only if it has one >imaginary frequency. Of course >(1)this alone does not prove it is the TS you are looking for, and >(2) at another level of calculation the TS may become a minimum or >hilltop. > >E Lewars A further clarification: I have frequently seen that the APPROXIMATE Hessian is used for this purpose, that is, the Hessian that has been built up from gradient information at various points during the optimization. Some programs will report the eigenvalues for this Hessian. However, many updating algorithms will make the approximate Hessian more "positive" than the real Hessian. The signs of eigenvalues of the approximate Hessian CANNOT be used for validation of ANYTHING. In addition, the real Hessian can also display negative eigenvalues for other reasons, especially if the gradient is not very close to zero. It is always a good idea to compare the frequencies before and after projection (Gaussian, for example, will allow this). The projection will remove the eigenvalues corresponding to translation and rotation. Even before projection, the corresponding frequencies should be very close to zero as long as the gradient is low (say, absolute values less than 10-20 cm-1). The remaining frequencies should not shift by more than 1-2 cm-1 after projection. If the shift is larger, a small negative eigenvalue may not be significant. Per-Ola Norrby * Per-Ola Norrby, Dept. of Med. Chem., Danish School of Pharm. * peo@dfh.dk, http://compchem.dfh.dk/PeO/ * tel. +45-35306506, fax +45-35306040 From chemistry-request@server.ccl.net Sat Nov 27 09:00:40 1999 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA18031 for ; Sat, 27 Nov 1999 09:00:33 -0500 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id SAA10495 for ; Sat, 27 Nov 1999 18:17:50 +0530 Received: (from gadre@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id SAA20586 for CHEMISTRY@www.ccl.net; Sat, 27 Nov 1999 18:44:23 +0530 Date: Sat, 27 Nov 1999 18:44:23 +0530 From: "Prof. Shridhar R. Gadre" Message-Id: <199911271314.SAA20586@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: hydration of anions Dear Friends: Can someone give us references of quantum chemical (as well as Monte Carlo etc.) studies of hydration of the following anions. F-, Cl-, CN-, NO2- and NO3-. Thanks a lot!.................................Shridhar Gadre From chemistry-request@server.ccl.net Sat Nov 27 17:53:07 1999 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 RAA20588 for ; Sat, 27 Nov 1999 17:53:06 -0500 Received: (qmail 23288 invoked from network); 27 Nov 1999 21:39:44 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 27 Nov 1999 21:39:44 -0000 Received: from egppp2.physics.upatras.gr by pythagoras.physics.upatras.gr with SMTP (1.36.108.4/16.2) id AA28336; Sat, 27 Nov 1999 23:37:53 GMT Message-Id: <000901bf1e4e$009f8580$5e9f8c96@stelios> From: "garoufal" To: Subject: CIS and disk usage in g94 Date: Sun, 24 Oct 1999 21:31:34 +0300 I have been trying to perform CIS calculation on a fairly bib system (i.e 35 heavy atoms) with gaussian 94. When I use the DIRECT option the computation is very time consuming but it will finish. When I use no keyword (which means it will perform a semi-direct calculation) the calculation goes on to the semi-direct transformation and although there is enough space in the disk, the program stops with the message "Error termination in NtrErr: NtrErr Called from FileIO." I have tried the maxdisk comand and I have also tried to split the .wrf file to several files. The program allways stops at the same point. Any ideas? Is there something I am not doing right? or it is a limitiation of the program concerning the CIS calculations? thanks in advance ____________________________________ Christos S. Garoufalis Dept. of Physics, University of Patras, Greece