From owner-chemistry@ccl.net Thu Oct 25 00:05:00 2007 From: "Jan Labanowski janl**speakeasy.net" To: CCL Subject: CCL: Charles Frederick Bender, 1940-2007 Message-Id: <-35482-071024205051-20149-sfdnNtxHobyD4rTIjrVxvw=server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 25 Oct 2007 00:50:38 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl+*+speakeasy.net] I am sorry for being to impulsive and sending a message about passing of my former boss and friend too early. I wish it to be a good sign, though my hopes are really low. I received the message below later today from Dr. Pritchard. I am sending it to you as soon as possible, so you do not do what I did, i.e., announce the death of the living person. > ** High Priority ** > > I am writing to update you all on Charlie Bender. As you know, I sent a note early > yesterday morning after speaking with Charlie's caregiver. She told me that he had > passed away. She indicated that information was from his doctor. Since then, > another close friend of Charlie's called me to tell me that Charlie has not passed > away. After several unreturned calls to his caregiver, I called the hospital where > I thought Charlie might be staying. I reached Charlie's brother-in-law in the > intensive care unit. He says that Charlie has not passed away; but he is gravely > ill and is not expected to live. That is all I know at this point. He is simply in > my prayers now. > > Please accept my heartfelt apologies for the miscommunication. I acted in good > faith after receiving information that I believed was accurate. Charlie's > brother-in-law will contact me if Charlie's condition changes. > > Dr. Richard H. (Dick) Pritchard (Col, USAF - Ret) > Director, Federal Programs, OSC > Deputy Program Director, MOS Consortium, DoD High Performance > Computing Modernization Program (HPCMP), User Productivity > Enhancement and Technology Transfer (PET) > Secretary/Treasurer, Coalition for Academic Scientific Computing > > The Ohio Supercomputer Center (OSC) > 1224 Kinnear Road > Columbus, OH 43212-1163 > Cell 614.440.4641 Office 614.292.1163 Fax 614.292.7168 > rhp-,-osc.edu > From owner-chemistry@ccl.net Thu Oct 25 03:58:00 2007 From: "Yangsoo Kim vsmember_+_gmail.com" To: CCL Subject: CCL:G: Geometry optimization software ? Message-Id: <-35483-071025034237-9530-meC3g8npnRouv/3MAnwigw++server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Thu, 25 Oct 2007 16:35:38 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember]~[gmail.com] Dear All, I'm wondering if there is any information showing today's available software that performs geometry optimization efficiently. Particularly, I'm interested in an optimizer that considers finding global minimum by performing constrained optimization. I'm getting several optimized structures without imaginary frequency from Gaussian03 runs, but finally found to be the structures from local minima. So, I'm looking for some optimizers that are not included in the G03. I would greatly appreciate if you could drop me a line with the name of software showing good performance for the global geometry optimization. Many thanks in advance and I'll summarize the replies on request. Yangsoo Kim, Ph.D. From owner-chemistry@ccl.net Thu Oct 25 05:38:00 2007 From: "Pierre Archirel pierre.archirel::lcp.u-psud.fr" To: CCL Subject: CCL:G: point charges in Gaussian Message-Id: <-35484-071025050726-4222-DtAmMLLO0lDDc3/R3Evatg{=}server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 25 Oct 2007 11:25:21 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel\a/lcp.u-psud.fr] Dear collegue. Point charges can be defined with the keyword: # ... charge... after the geometry you put one charge per line: x y z q and terminate with a blank line, so that you need not give the number of charges. This is given in the G03 manual, page 60 P.A. __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel[-]lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Thu Oct 25 06:01:00 2007 From: "Pierre Archirel pierre.archirel*o*lcp.u-psud.fr" To: CCL Subject: CCL:G: global optimisation Message-Id: <-35485-071025052535-5907-i+4RBasfmu52Bizt2+ngqA*server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 25 Oct 2007 11:43:35 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel^lcp.u-psud.fr] Dear Yangsoo Kim, I am afraid you mistake local minima and transition states: 1- imaginary frequencies caracterise points that are not minimas, like saddle points. 2- all the local minimas and the global minimum as well, do have real frequencies. 3- if your system has several local minimas, the only way to find the global one is to perform several optimisations with several starting points. If your system is big, force fields can help you in building these starting points. This job can be tedious, but can be done with g03. Best wishes, P.A. __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel_-_lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Thu Oct 25 10:11:00 2007 From: "Sina T reli sinatureli%%gmail.com" To: CCL Subject: CCL: Optimizing A Molecule In Complex Message-Id: <-35486-071025085416-1515-lqcYtQU6pCDssK4bWuJCYQ() server.ccl.net> X-Original-From: "Sina T reli" Date: Thu, 25 Oct 2007 08:54:12 -0400 Sent to CCL by: "Sina T reli" [sinatureli{=}gmail.com] Hello, I am trying to minimize a molecule with in its surrounding protein. However because orbital conjugations are important in this molecule I need to use semi-empirical methods. And thus I try to pick the minimal enviroment that will mimic the whole protein (in other words the pocket and fixing those atoms to their coordinates). However when I minimize the molecule alone and with in the pocket that I defined, the results are very similar in terms of molecular shape and spectroscopic properties. In short the protein enviroment seems to have little effect on the shape of the molecule when I try to do optimization with a molecular modelling program. Is simply doing this not enough to mimic the effect of the protein environment, would you propose another method? By the way I am using mopac 2007 pm6 and mndo/d methods. Thanks... From owner-chemistry@ccl.net Thu Oct 25 11:37:00 2007 From: "Jimmy Stewart MrMOPAC(0)att.net" To: CCL Subject: CCL: Access to the J. of Mol. Mod is now free. Message-Id: <-35487-071025102032-16020-vT9UqPQ0dFwthJqJeFZvaw]-[server.ccl.net> X-Original-From: Jimmy Stewart Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 25 Oct 2007 07:46:10 -0600 Mime-Version: 1.0 Sent to CCL by: Jimmy Stewart [MrMOPAC- -att.net] I was surprised to find that on-line access to articles in J. Mol. Mod: http://www.springerlink.com/content/100529/ is now free. Apparently, Springer has opened all of J. Mol. Model. up for a few weeks as a marketing measure. If you want any of the articles, now's the time to download them! Jimmy ( /a\ /a\ ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: MrMOPAC/a\OpenMOPAC.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | http://openmopac.net/ | | USA | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200| | .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo.| | .-----------------------\ (----( )---------------------------------------. \_) ) / (_/ From owner-chemistry@ccl.net Thu Oct 25 13:55:01 2007 From: "CCL CCL computationalchemist[a]gmail.com" To: CCL Subject: CCL: Ag:Si(111) Surface Message-Id: <-35488-071025134844-30699-Dz/DSR6zbs1p1wuH+j+Abw[A]server.ccl.net> X-Original-From: "CCL CCL" Content-Type: multipart/alternative; boundary="----=_Part_2786_20833038.1193334107844" Date: Thu, 25 Oct 2007 18:41:47 +0100 MIME-Version: 1.0 Sent to CCL by: "CCL CCL" [computationalchemist{:}gmail.com] ------=_Part_2786_20833038.1193334107844 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Folks, Could anyone help me with coordinates for Si(111) reconstructed surfaces. any help would be acknowledged. Thanks in advance -- Regards, Dr. Sanjay ------=_Part_2786_20833038.1193334107844 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Folks,
Could anyone help me with coordinates for Si(111) reconstructed surfaces.
any help would be acknowledged.
Thanks in advance
--
Regards,
Dr. Sanjay ------=_Part_2786_20833038.1193334107844--