From ep7@dent.okayama-u.ac.jp Fri Jul 17 01:31:02 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA12040 Fri, 17 Jul 1998 01:30:57 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id OAA23155 for ; Fri, 17 Jul 1998 14:31:40 +0900 (JST) Message-Id: <199807170531.OAA23155@deews1.dent.okayama-u.ac.jp> Date: Fri, 17 Jul 1998 14:48:39 +0900 To: CHEMISTRY@www.ccl.net Subject: x,y,z vs. internal coordinates MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: I ask about the following. (1) The optimization using x,y,z coordinates is faster than that using internal coordinates. (2) Do you experience that the optimization using x,y,z coordinates converges unexpected optimized structure ? The optimization using internal coordinates is more safe than the optimization using x,y,z coordinates ? Thank you. From dino@eik.bme.hu Fri Jul 17 04:52:00 1998 Received: from goliat.eik.bme.hu (root@goliat.eik.bme.hu [152.66.250.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA13063 Fri, 17 Jul 1998 04:51:59 -0400 (EDT) Received: from localhost (dino@localhost [127.0.0.1]) by goliat.eik.bme.hu (8.8.8/8.8.8) with SMTP id KAA04224 for ; Fri, 17 Jul 1998 10:51:52 +0200 (MET DST) Date: Fri, 17 Jul 1998 10:51:51 +0200 (MET DST) From: SZIEBERTH Denes To: chemistry@www.ccl.net Subject: fermi contact Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL-ers, Could someone explain to me how the values appearing in the fermi contact analysis section of a G94 output computed in the UHF, UMP2, UCISD and UCCSD cases? Denes Szieberth dino@goliat.eik.bme.hu From richard@tc.cornell.edu Fri Jul 17 08:46:18 1998 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA14825 Fri, 17 Jul 1998 08:46:17 -0400 (EDT) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id IAA33851; Fri, 17 Jul 1998 08:46:17 -0400 Sender: richard@tc.cornell.edu Message-ID: <35AF4798.1CFB@tc.cornell.edu> Date: Fri, 17 Jul 1998 08:46:16 -0400 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net CC: ep7@dent.okayama-u.ac.jp Subject: Re: CCL:x,y,z vs. internal coordinates References: <199807170531.OAA23155@deews1.dent.okayama-u.ac.jp> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have heard arguments on both sides. One the one hand, optimization steps taken in torsion space are thought by many to follow more closely the natural low energy pathways in molecules, or at least in proteins. This argument seems to be backed up by recent numerical experiments in Ruben Abagyan's group: Abagyan R.A. and Totrov, M.M. J. Mol. Bio 235 (1994) 983 (which admittedly I have not read), in which they measure how far one can move away from a local minimum and still return via optimization. Others argue that by restricting the conformational search to torsion space, the energy barriers are made higher and the search space becomes "topologically" more complex as a result. Note that the ECEPP forcefield used by Abagyan has adjusted torsional barrier heights, supposedly to compensate for this. Personally, I think this is comparing apples with oranges until someone can perform an optimization in ALL internal coordinates (including bends, stretches etc. but excluding redundant coordinates) so that the number of degrees of freedom are the same. I suspect, however, that internal coords will win for the reasons stated above. Anybody know of a progam that can do FULL internal coordinate optimization? Richard Gillilan Cornell Theory Center > I ask about the following. > > (1) The optimization using x,y,z coordinates is faster than that using > internal coordinates. > > (2) Do you experience that the optimization using x,y,z coordinates > converges unexpected optimized structure ? The optimization using > internal coordinates is more safe than the optimization using x,y,z > coordinates ? > > Thank you. From segalemb@usp.br Fri Jul 17 10:01:57 1998 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA15651 Fri, 17 Jul 1998 10:01:53 -0400 (EDT) Received: from localhost by swan2.uspnet.usp.br (SMI-8.6/SMI-SVR4) id KAA06214; Fri, 17 Jul 1998 10:56:55 -0300 Date: Fri, 17 Jul 1998 10:56:55 -0300 (EST) From: Sergio Emanuel Gelembeck X-Sender: segalemb@swan2 To: Thomas Nowak cc: Alan Shusterman , chemistry@www.ccl.net Subject: Re: CCL:CCL: SUMMERY Energy analysis? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Thomas, I don't know what you need, but there is at least four different methods of analysis of interactions: - NBO, from Weinhold. It is found in Gaussian. - Morokuma, found in GAMESS. - AIM, from Bader. The program can be obtained with the author. - In GAMESS there is another type of analysis form Jansen and Gordon. Best, Sergio From hinsen@dirac.cnrs-orleans.fr Fri Jul 17 10:35:51 1998 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA15831 Fri, 17 Jul 1998 10:35:48 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.7/8.7) id QAA41584; Fri, 17 Jul 1998 16:35:23 +0200 (DFT) Date: Fri, 17 Jul 1998 16:35:23 +0200 (DFT) Message-Id: <199807171435.QAA41584@dirac.cnrs-orleans.fr> From: Konrad Hinsen To: chemistry@www.ccl.net Subject: Version 1.2b1 of the Molecular Modeling Toolkit is available Update: The Molecular Modeling Toolkit, version 1.2b1 ===================================================== The Molecular Modelling Toolkit (MMTK) is a program library for molecular simulation and modelling applications. Its aim is to provide researchers, especially those working on the development of new modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling. MMTK is free software. The new release 1.2b1, adds new features and improvements. Some highlights: - Fast-multipole electrostatics via the DPMTA library. - Additional C-alpha-only protein model for faster analysis. - Faster energy evaluation. - Numerically stable SVD-based charge fitting procedure. - Enhanced visualization functions. For details and for downloading, check the MMTK home page: http://starship.skyport.net/crew/hinsen/mmtk.html -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From cwong@sugen.com Fri Jul 17 16:27:54 1998 Received: from sugen1.sugen.sf.ca.us (sugen1.sugen.sf.ca.us [192.152.9.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA18441 Fri, 17 Jul 1998 16:27:53 -0400 (EDT) Received: from octane (octane [192.152.9.33]) by sugen1.sugen.sf.ca.us (8.8.6/8.8.6) with SMTP id NAA16157 for ; Fri, 17 Jul 1998 13:36:01 -0700 (PDT) Sender: cwong@sugen1.sugen.sf.ca.us Message-ID: <35AFB303.41C6@sugen.com> Date: Fri, 17 Jul 1998 13:24:35 -0700 From: Chung Wong X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: subscription Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Is this the address for subscription to the Computational Chemistry Discussion Forums? Thanks......Chung Wong From MARYJO@neu.edu Fri Jul 17 18:54:38 1998 Received: from NUHUB.DAC.NEU.EDU (nuhub.dac.neu.edu [129.10.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA19470 Fri, 17 Jul 1998 18:54:37 -0400 (EDT) From: MARYJO@neu.edu Received: from neu.edu by neu.edu (PMDF V5.1-8 #24746) id <01IZIMYEC7GWADG67P@neu.edu> for chemistry@www.ccl.net; Fri, 17 Jul 1998 18:54:33 EST Date: Fri, 17 Jul 1998 18:54:33 -0500 (EST) Subject: gradients To: chemistry@www.ccl.net Message-id: <01IZIMYEDJOYADG67P@neu.edu> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Hello everybody. It has been a long time since I wrote a program myself to calculate the gradient of a function, and am hoping that some of you experts out there can help me. Here is my very simple problem: I have a 3-D space and can calculate the value of the function at any sets of points in the space that I choose. I must calculate the gradient of my function. Can anybody give me some pointers about the best way to do this (both in terms of comnputational efficiency and accuracy)? Is it best to take a rectangular 3-D box and space the points evenly? Is there a numerical recipe book with an efficient routine to get the gradient? Would appreciate any helpful advice or comments. Thanks in advance, Mary j.o.