From chemistry-request@server.ccl.net Thu May 1 08:36:28 2003 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h41Ca9V02064 for ; Thu, 1 May 2003 08:36:15 -0400 Received: from njuitccwx (jproxy.nju.edu.cn [202.119.32.27]) by smtp01.sohu.com (Postfix) with ESMTP id E2F2EBA01 for ; Thu, 1 May 2003 20:13:12 +0800 (CST) Date: Thu, 1 May 2003 20:36:37 +0800 From: wxin To: "chemistry@ccl.net Subject: about CASSCF in G98 X-mailer: FoxMail 3.11 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20030501121312.E2F2EBA01@smtp01.sohu.com> Dear CCL-lister, when I used the Gaussian98 to do casscf geometry optimization calculation I encounter a serious problem.At the first point of the optimization, the wavefunction has converged to the desired state, but at the second point, the calculation converged to a state that is much higher in energy than the first point(several hatree). Who can tell me how to solve this problem? Thanks in advance. Wang Xin Dept Chem, Nanjing Univ P.R.China From chemistry-request@server.ccl.net Wed Apr 30 22:19:08 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h412J8V14253 for ; Wed, 30 Apr 2003 22:19:08 -0400 Received: from [24.65.168.211] ([24.65.168.211]) by cascara.uvic.ca (8.12.9/8.12.9) with ESMTP id h412Ixdg510712 for ; Wed, 30 Apr 2003 19:19:00 -0700 From: Roy Jensen To: Subject: SUMMARY: G03W multiprocessor support? Date: Wed, 30 Apr 2003 19:19:20 -0700 Message-ID: X-Mailer: Forte Agent 1.91/32.564 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h412J8V14254 All I received a response from Gaussian. The answer is NO, G03W does not support multiple processors. From previous discussion on CCL regarding G98W, you can have multiple instances of Gaussian on the same computer (you must purchase a license for ever instance) and Windows will [hopefully] assign each job to a different processor. (Search the archives for more information.) Regarding my comment that Gaussian was not responding, it appears they never received them -- they are usually good at responding. I am in contact with them off-list (unless, of course, they don't get my emails!! Roy Jensen On Wed, 30 Apr 2003 12:05:31 -0400 (EDT), Gaussian wrote: > > Dr. Jensen, > > > There was hope that the next version of Gaussian, G03W, would support > > multiple processors. I couldn't find anything on the Gaussian website, nor > > has Gaussian answered my emails. Does anyone know if it can? > > We have not added multiprocessor support to G03W or to G03M. When > we do this will be noted on the product description. > > I am curious about your comment that we have not answered your > E-mail. I don't have any messages from you on this topic. When did > you send them? I don't think we have been losing mail messages but > want to make sure. > Roy Jensen -----BEGIN PGP PUBLIC KEY BLOCK----- Comment: available at www.consol.ca ------END PGP PUBLIC KEY BLOCK------ From chemistry-request@server.ccl.net Thu May 1 03:18:50 2003 Received: from mail.shcnc.ac.cn ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h417ImV16984 for ; Thu, 1 May 2003 03:18:49 -0400 Received: from pc29 ([202.127.19.62]) by mail.shcnc.ac.cn (8.12.1/8.12.1) with SMTP id h41NLHa5011847 for ; Thu, 1 May 2003 16:21:17 -0700 (PDT) Message-Id: <200305012321.h41NLHa5011847@mail.shcnc.ac.cn> Date: Thu, 1 May 2003 15:19:55 +0800 From: Jinzhi Tan Reply-To: jztan@mail.shcnc.ac.cn To: ccl Subject: water in CHARMM Organization: SIMM-DDDC X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h417IoV16985 Dear Sir: I generate a huge box containing about 15,000 waters. I put my protein into the waters and delete the overlapped waters. In doing so, I encouter a lot of questions. First, how many waters should I delete? just 2~3 angstroms around the protein? Second, how to define the boundary conditions? When I try to equilibrate the water and protein, two waters fly away from the box. I don't know how to deal with the two water. Third, when I try to continue to equilibrate the system, the two water are much farther than before and the box are translation to the opposite directory. Thank you very much! Jinzhi Tan 2003-5-1 ************************************* Jinzhi Tan Ph.D. student Chinese Academy of Sciences Shanghai 200000, China Phone :086-21-64311833-507 Fax :086-21-64318401 E-mail:jztan@mail.shcnc.ac.cn tanjinzhi@hotmail.com ************************************* From chemistry-request@server.ccl.net Thu May 1 07:35:06 2003 Received: from mail.shcnc.ac.cn ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h41BZ4V00551; Thu, 1 May 2003 07:35:05 -0400 Received: from pc29 ([202.127.19.62]) by mail.shcnc.ac.cn (8.12.1/8.12.1) with SMTP id h423bWa5015237; Thu, 1 May 2003 20:37:32 -0700 (PDT) Message-Id: <200305020337.h423bWa5015237@mail.shcnc.ac.cn> Date: Thu, 1 May 2003 19:36:13 +0800 From: Jinzhi Tan Reply-To: jztan@mail.shcnc.ac.cn To: ccl CC: "chemistry-request@server.ccl.net" Subject: charges and ions in CHARMM Organization: SIMM-DDDC X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h41BZ6V00552 Dear Sir: I generate a water box and put the protein into the box. The whole system have five positive charges. I know I must neutralize the charges, but I don't know how to add the ions(such as Cl-) into the system. How can I complete this process? Thank you very much! Best wishes, Jinzhi Tan 2003-5-1 ************************************* Jinzhi Tan Ph.D. student Chinese Academy of Sciences Shanghai 200031, China Phone :086-21-64311833-507 Fax :086-21-64318401 E-mail:jztan@mail.shcnc.ac.cn tanjinzhi@hotmail.com ************************************* From chemistry-request@server.ccl.net Thu May 1 13:27:08 2003 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h41HR5V12002 for ; Thu, 1 May 2003 13:27:06 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.7/TSRI-4.1rx) with SMTP id h41HR5E18247 for ; Thu, 1 May 2003 10:27:05 -0700 (PDT) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 5142; Thu, 01 May 2003 10:25:01 -0700 (PDT) Received: from renoir.scripps.edu (renoir [137.131.252.25]) by relay1.scripps.edu (8.11.7/TSRI-4.2rAV) with ESMTP id h41HP5S23295; Thu, 1 May 2003 10:25:05 -0700 (PDT) Received: by renoir.scripps.edu (Postfix, from userid 1376) id 4DB5FF8C; Thu, 1 May 2003 10:25:05 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by renoir.scripps.edu (Postfix) with ESMTP id 450A5B5A; Thu, 1 May 2003 10:25:05 -0700 (PDT) Date: Thu, 1 May 2003 10:25:05 -0700 (PDT) From: Michael Crowley To: Jinzhi Tan Cc: ccl Subject: Re: CCL:water in CHARMM In-Reply-To: <200305012321.h41NLHa5011847@mail.shcnc.ac.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Jinshi, I think you might benefit from the tutorials found on the following page. They are not very verbose or explanatory but do provide a working set of scripts for solvating and equilibrating several different systems. http://www.psc.edu/general/software/packages/charmm/tutorial/index.html Mike ----------------------------------------------------------------- Physical mail: Dr. Michael F. Crowley Department of Molecular Biology, TPC6 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037 Electronic mail: crowley@scripps.edu Telephone: 858/784-9290 Fax: 858/784-8688 -----------------------------------------------------------------