From owner-chemistry@ccl.net Sun Sep 24 00:04:09 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id XAA04307; Sat, 23 Sep 1995 23:52:25 -0400 Received: from csb0.IPC.PKU.EDU.CN for ldw@csb0.IPC.PKU.EDU.CN by bedrock.ccl.net (8.6.10/950822.1) id XAA08896; Sat, 23 Sep 1995 23:52:20 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@ccl.net id AA18354; Sun, 24 Sep 95 11:32:44 -0700 Date: Sun, 24 Sep 1995 11:32:43 -0700 (PDT) From: ldw To: chemistry@ccl.net Subject: Re: CCL:Call for Papers - 3D databasing In-Reply-To: <199509201515.IAA05403@paganini.ba.msi.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I want to the molecular dynamics calculation of small peptides(lenght 5 to 8). Before I set out to do the calculations, I like to listen any of your suggests or experences. To describe in detail is warmly welcome, such as how many steps will equlibration take, how long time will be enought to get a reasonable structure. The newly references are also welcome. I will summary if some thing interesting. Thanks in advance, Dawei ---------- *** Dawei LIN *** ------------------ Ph.D student of Molecular Design Lab Institute of Physical chemistry Peking University Beijing 100871 P.R.China Phone: 86-10-2501490 Fax: 86-10-2501725 Email: ldw@ipc.pku.edu.cn ldw@pschnetware.pku.edu.cn URL: http://www.ipc.pku.edu.cn/ldw/ldw.htm ------------------------------------------------ From owner-chemistry@ccl.net Sun Sep 24 06:49:14 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA06791; Sun, 24 Sep 1995 06:35:46 -0400 Received: from csb0.IPC.PKU.EDU.CN for ldw@csb0.IPC.PKU.EDU.CN by bedrock.ccl.net (8.6.10/950822.1) id GAA10065; Sun, 24 Sep 1995 06:35:41 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@ccl.net id AA19332; Sun, 24 Sep 95 18:15:59 -0700 Date: Sun, 24 Sep 1995 18:15:55 -0700 (PDT) From: ldw To: chemistry@ccl.net Subject: Small Peptides Dynamics Calculation Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am SORRY for a wrong subject of my first posting of the following message. (The wrong subject is CCL:Call for Papers - 3D databasing, if you have read that message. Not need to read the following). :-( I want to the molecular dynamics calculation of small peptides(lenght 5 to 8). Before I set out to do the calculations, I like to listen any of your suggests or experences. To describe in detail is warmly welcome, such as how many steps will equlibration take, how long time will be enought to get a reasonable structure. The newly references are also welcome. I will summary if some thing interesting. Thanks in advance, Dawei ---------- *** Dawei LIN *** ------------------ Ph.D student of Molecular Design Lab Institute of Physical chemistry Peking University Beijing 100871 P.R.China Phone: 86-10-2501490 Fax: 86-10-2501725 Email: ldw@ipc.pku.edu.cn ldw@pschnetware.pku.edu.cn URL: http://www.ipc.pku.edu.cn/ldw/ldw.htm ------------------------------------------------ From bartberg@chem.ufl.edu Sun Sep 24 12:04:18 1995 Received: from server for bartberg@chem.ufl.edu by www.ccl.net (8.6.10/950822.1) id LAA07858; Sun, 24 Sep 1995 11:59:58 -0400 Received: by server (5.x/4.11) id AA13805; Sun, 24 Sep 1995 11:54:26 -0400 Date: Sun, 24 Sep 1995 11:54:25 -0400 (EDT) From: "Michael D. Bartberger" To: Computational Chemistry List Subject: Spin Contamination in Correlated Optimizations Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all: A while back I posted a question regarding regarding spin-projected energies vs. non-, and UHF vs. ROHF in doing optimizations on systems where spin contamination is relatively high. I summarized these responses and the interested reader can find these in the archives. Let me extend this one step further...... it was mentioned that UMPn optimizations using a spin-contaminated reference can lead to terrible geometries...... I have also seen this comment given in various texts and papers, although no examples are given. I would like to hear from readers who have experienced this for themselves. Any references, pointers, or "personal accounts" would be appreciated. We do computational studies on fluorinated radicals, and spin contamination in the UHF wavefunction is often quite high. I have usually stayed with UHF geometries, even on systems small enough where MPn optimizations might be feasible. I'd like to collect some more ammunition on this subject. Thanks!!! Regards, Michael ________________________________________________________________________________ Michael D. Bartberger bartberg@chem.ufl.edu TEL: (904) 392-3580 Department of Chemistry bartberg@qtp.ufl.edu FAX: (904) 846-0296 University of Florida Gainesville, FL 32611 USA ________________________________________________________________________________ From owner-chemistry@ccl.net Sun Sep 24 18:19:23 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA11372; Sun, 24 Sep 1995 18:14:37 -0400 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by bedrock.ccl.net (8.6.10/950822.1) id SAA12037; Sun, 24 Sep 1995 18:14:36 -0400 Received: from rainbow.uchicago.edu (rainbow.uchicago.edu [128.135.136.33]) by midway.uchicago.edu (8.6.10/8.6.4) with SMTP id RAA17300 for <@midway.uchicago.edu:chemistry@ccl.net>; Sun, 24 Sep 1995 17:14:36 -0500 Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA15634; Sun, 24 Sep 95 17:14:29 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9509242214.AA15634@rainbow.uchicago.edu> Subject: Small Peptide Dynamics To: chemistry@ccl.net Date: Sun, 24 Sep 1995 17:14:28 -0500 (CDT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1539 Dawei Lin writes.. > > I want to do molecular dynamics calculation of small peptides(lenght 5 > to 8). Before I set out to do the calculations, I like to listen any of > your suggests or experences. To describe in detail is warmly welcome, > such as how many steps will equlibration take, how long time will be > enought to get a reasonable structure. The newly references are also welcome. >I will summary if some thing interesting. Some papers by Karl Freed and Graham Flemming at the University of Chicago discuss this problem. (See, for instance, the special issue of Chemical Physics on Protein Dynamics Vol 158 (#2,3) 15 December 1991 A paper by Freed and others recently appeared in the Journal of Chemical Physics which compares MD simulations on a small peptide with experimental flouresence depolarization which measure the orientational relxation times of the absorbing side group. The MD simulations fail to reproduce the experimental relxation time, severely overestimating the relaxation time. Given these results, at this point it is unclear to me whether the potentials used in MD simulations can truly represent the dynamics of small peptides and proteins. I have been tracking down detailed comparisons between MD simulations and dymanics experiments to answer this. I would be most interested in reading other opinions and seeing other pieces of evidence, pro and/or contrary. Anyone? Chuck Martin Theoretical Biophysics The Beckman Institute The University of Illionis at Urbana-Champaign