From chemistry-request@ccl.net Fri Oct 17 00:15:41 2003 Received: from ccl.net (email.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9H4F8dH013586 for ; Fri, 17 Oct 2003 00:15:09 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id h9H4EjMX015397; Fri, 17 Oct 2003 00:14:45 -0400 Date: Fri, 17 Oct 2003 00:14:07 -0400 (EDT) From: "Dr. Jan K Labanowski" To: chemistry~at~ccl.net, microelectronics~at~atomicscaledesign.net cc: jkl~at~ccl.net, korkin~at~nanoandgiga.com Subject: Nov. 13-15 US-Russian Workshop on Bridging Atomic and Macroscopic Scales, Phoenix, AZ Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Subscribers, Program is being finalized for the: US-Russian Workshop on Software Development (SWN2003) Bridging atomic and macroscopic scales for materials, process, and device design November 13-15, 2003 Arizona State University, Tempe, AZ, U.S.A. http://asdn.net/swn2003 You are wholeheartedly invided to participate by your list coordinator. If you would like to attend, please register at the Webside above. Overview of the workshop follows. It may be quite convenient to those who are also interested in attending Supercomputing 2003. Jan Workshop oberverview: Computer modeling and simulation continues to have increasing impact on process, material, and device design, eliminating a significant amount of experimental work based on a trail-and-error approaches and reducing the costs of the products and technologies. However, incorporation of atomic and molecular scale information into simulations of macroscopic systems remains a challenge. Opportunities exist for the development of integrated software tools that bridge the atomic and macroscopic scales, to enable solutions to complex scientific and technological problems. This workshop will bring together scientists and software designers who are working in the area of process, material and device design on the atomic scale with a particular focus on computation and predicting measurable macroscopic characteristics. One goal of the workshop is to stimulate an active collaboration and partnership between scientists and software designers in developing the integrated tools and interfaces between computer programs, which will allow the incorporation of atomic-scale information in macroscopic simulations in an efficient and reliable manner. Another aim of the workshop is to explore opportunities for developing the expertise of scientists and engineers in the US and Russia, former nuclear rivals, in the area of theoretical material science to promote science, education and cooperation in non-military technological areas. Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl~at~ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ From chemistry-request@ccl.net Fri Oct 17 00:50:30 2003 Received: from nankai.edu.cn (sun.nankai.edu.cn [202.113.16.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9H4nodH014105 for ; Fri, 17 Oct 2003 00:49:54 -0400 Received: (eyou send program); Fri, 17 Oct 2003 12:50:31 +0800 Received: from unknown (HELO 192.168.0.101) (unknown@128.195.87.184) by 202.113.16.21 with SMTP; Fri, 17 Oct 2003 12:50:31 +0800 Date: Thu, 16 Oct 2003 21:49:27 -0700 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <1455746254.20031016214927.-at-.joyie.com> To: gaussian.com!csd.-at-.gaussian.com (Cust. Service Doug) CC: chemistry.-at-.ccl.net Subject: Re[4]: CCL:GDIIS and Z-MATRIX In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.8 required=7.0 tests=EMAIL_ATTRIBUTION,FROM_ENDS_IN_NUMS,IN_REP_TO, QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Cust., It does help me a lot. I used Int=ultrafine and opt=calcall, with tight option. although the RMS Displacement still didn't reach the threshold, the RMS force reached. I need to perform a freq calculation to make sure it is a minimum. Now all the distances between neighbor oxygens are the same (4 water cluster). The distances beteen O-H and O...H are also the same. Thank you very much. Best regards John Lee Wednesday, October 15, 2003, 9:13:24 AM, you wrote: CSD> My guess is that it was hard because the Berny algorithm needed CSD> to have the integration quality improved to go along with the tighter CSD> integration criteria and the small forces involved in these clusters. CSD> In such a case I am dubious that GDIIS is really giving you a "better" CSD> structure, but I can believe it is willing to claim the criteria CSD> are met. It deals better with inaccuracies in the gradient and so CSD> I have suggested its use with solvation models and as you can see from CSD> the manual with semi-empirical models. CSD> To use the Z-matrix I would recommend you try a couple of CSD> approaches. First use Int=Ultrafine and see if OPT=Tight does not CSD> behave better. Second, I would suggest doing this as OPT=(CalcFC,Tight) CSD> if you are starting close to an optimized structure. Or possibly CSD> OPT=(CalcAll,Tight) because the force constants here are small and CSD> it is vital to have them correct for the optimization to work. >> >> Hi Cust., >> >> I the simulation of 4-8 water cluster, I want to keep all the >> distances between neighbor oxygen the same. However it was hard to >> converge with B3LYP 6-311++G** and tight if I didn't use GDIIS. If I use GDIIS >> the distances will not be the same. >> >> Thanks for your reply. >> >> John >> >> Tuesday, October 14, 2003, 5:27:52 PM, you wrote: >> >> >> CSD> John, >> >> CSD> Why do you need to use GDIIS? >> >> CSD> Note that this would break symmetry only if you are using the Z-matrix >> CSD> to define symmetry which is not really in the molecule? >> >> >> >> >> >> Hi CCLers, >> >> >> >> Z-matrix optimization only work with Berny algorithm. >> >> What if I have to use GDIIS and still want to control the zmatrix >> >> symmetry. Is there a way to do it? >> >> >> >> >> >> >> >> -- >> >> Best regards, >> >> John >> >> >> >> >> >> >> >> -= This is automatically added to each message by the mailing script =- >> >> To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >> >> and send your message to: CHEMISTRY.-at-.ccl.net >> >> >> >> Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net >> >> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs >> >> >> >> If your mail is bouncing from CCL.NET domain send it to the maintainer: >> >> Jan Labanowski, jkl.-at-.ccl.net (read about it on CCL Home Page) >> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> Best regards, >> John Lee >> From chemistry-request@ccl.net Fri Oct 17 06:01:35 2003 Received: from antivirus.9netweb.it (av.9netweb.it [66.71.191.45]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9HA13dH021366 for ; Fri, 17 Oct 2003 06:01:04 -0400 Received: from Debug (localhost.9netave.it [127.0.0.1] (may be forged)) by antivirus.9netweb.it (8.10.1/8.11.6) with SMTP id h9H8G8A43543 for ; Fri, 17 Oct 2003 10:16:08 +0200 (CEST) (envelope-from meeting2004^at^moldiscovery.com) Message-Id: <200310170816.h9H8G8A43543^at^antivirus.9netweb.it> To: chemistry^at^ccl.net From: meeting2004^at^moldiscovery.com Subject: 1st Molecular Discovery User Meeting Date: Fri, 17 Oct 2003 10:16:08 +0200 CET X-Mailer: Endymion MailMan Standard Edition v3.0.20 X-Spam-Status: No, hits=4.5 required=7.0 tests=FROM_ENDS_IN_NUMS,INVALID_DATE,MAILTO_TO_SPAM_ADDR, MSG_ID_ADDED_BY_MTA_3,NO_REAL_NAME,OPPORTUNITY_2 version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Novel Computational Methods for Rational Drug Design, ADME and DMPK Prediction, Cheminformatics. We are pleased to announce the first MD Users meeting which will be held in Perugia, Italy, from the 18th to 22nd of May, 2004. The main focus of the meeting will be on the practical use of the MD programmes in real research applications, and participants will be able to work with the latest release of each programme. They will also have a unique opportunity to evaluate and criticize some of the novel software projects which are currently being developed by the scientists at Molecular Discovery. Feedback and suggestions from all participants will be greatly appreciated, so that our future programmes can be as useful, reliable and effective as possible. Lectures, Case Work and Computer Studies will be given by: * Dr. Peter Goodford (the father of the well-known GRID force field). * Prof. Gabriele Cruciani, showing practical applications of MIFs in ADME, DMPK, SBDD * Prof. Manuel Pastor, on 3D-QSAR grid-independent methods * Prof. Tudor Oprea, reporting on the Penguins projects * Dr. Ismael Zamora, reporting of the MetaSite project * Dr. Massimo Baroni, the author of our main cheminformatic tools * Dr. Silvio Mecucci, the VolSurf project developer * Dr. Emanuele Carosati, Dr. Paolo Benedetti, Dr. Gianluca Sforna, Dr. Riccardo Vianello on practical Case Works The number of attendees is limited, so a definitive registration should be made as soon as possible. The meeting will take place at the Relais San Clemente resort. It is "an old noble residence named after che millenary church which forms part of the complex" located near Perugia in "an atmosphere of suggestive naturalness". More info: http://www.moldiscovery.com/meeting2004.php ---------------------------------- - Molecular Discovery Ltd. - - meeting2004^at^moldiscovery.com ---------------------------------- From chemistry-request@ccl.net Fri Oct 17 06:13:04 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9HACWdH021589 for ; Fri, 17 Oct 2003 06:12:32 -0400 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 1AARaw-0002SW-MG; Fri, 17 Oct 2003 11:12:30 +0100 Received: from matpc18.mats.qmw.ac.uk ([138.37.43.64] helo=Ruzhen) by smtp.qmul.ac.uk with smtp (Exim 3.35 #5) id 1AARau-0001Bd-00; Fri, 17 Oct 2003 11:12:28 +0100 Message-ID: <06f101c39497$6a868840$402b258a@Ruzhen> From: "Ru-Zhen Li" To: Cc: "W Smith" Subject: how to get the utility sub-directory of DL-POLY? Date: Fri, 17 Oct 2003 11:14:14 +0100 MIME-Version: 1.0 Content-Type: multipart/related; type="multipart/alternative"; boundary="----=_NextPart_000_06ED_01C3949F.CC359380" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Sender-Host-Address: 138.37.43.64 X-QM-Scan-VirusCheck: clean X-Spam-Status: No, hits=0.2 required=7.0 tests=EXTRA_MPART_TYPE,HTML_60_70,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_06ED_01C3949F.CC359380 Content-Type: multipart/alternative; boundary="----=_NextPart_001_06EE_01C3949F.CC359380" ------=_NextPart_001_06EE_01C3949F.CC359380 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Fiesta Dear all, I am trying to use DL-POLY, version 2.14 for RH-Linux, after I installed = it, I found the utility sub-directory is missing, which contains a lot = of useful models such as genlat etc, helping to generate the CONFIG = input file, can anyone tell me how can I get it? Thanks a lot!! best regards, Ru-Zhen ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li)at(qmul.ac.uk Materials Department Queen Mary University of London E1 4NS ------=_NextPart_001_06EE_01C3949F.CC359380 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Fiesta

Dear all,
 
I am trying to use DL-POLY, version 2.14 for RH-Linux, after I = installed=20 it, I found the utility sub-directory is missing, which contains a lot = of useful=20 models such as genlat etc, helping to generate the CONFIG input file, = can anyone=20 tell me how can I get it?
 
Thanks a lot!!
best regards,
Ru-Zhen
********************************************************************= **
Ms=20 Ru-Zhen Li
 
0044-020-78826327
r.li)at(qmul.ac.uk
Materials=20 Department
Queen Mary
University of London
E1=20 4NS
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Gn/G2Tl/vlcf7iT/AGf62x6hVU9R8/4ZWUt4UP8A/9k= ------=_NextPart_000_06ED_01C3949F.CC359380-- From chemistry-request@ccl.net Fri Oct 17 04:24:38 2003 Received: from hitpro.hitachi.co.jp (hitpro.hitachi.co.jp [133.145.224.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9H8O5dH018564 for ; Fri, 17 Oct 2003 04:24:07 -0400 Received: from mc4.mcg.hitachi.co.jp by hitpro.hitachi.co.jp (8.12.9p1/eHI-hitpro) id h9H8O3Zb013251; Fri, 17 Oct 2003 17:24:03 +0900 (JST) Received: (from root@localhost) by mc4.mcg.hitachi.co.jp (8.11.6+Sun/8.11.6) id h9H8O2I18692 for ; Fri, 17 Oct 2003 17:24:02 +0900 (JST) Received: from unknown [192.168.2.1] by mc4.mcg.hitachi.co.jp with SMTP id TAA18690 ; Fri, 17 Oct 2003 17:24:01 +0900 Received: from navsg2.hitachi.co.jp by navsg2.hitachi.co.jp (8.9.3/3.7W-navsg2) id RAA03888; Fri, 17 Oct 2003 17:24:00 +0900 (JST) Received: from hul3.hitachi-ul.co.jp ([158.211.190.2]) by navsg2.hitachi.co.jp (NAVGW 2.5.2.17) with SMTP id M2003101717235925206 for ; Fri, 17 Oct 2003 17:23:59 +0900 Received: by hul3.hitachi-ul.co.jp (8.11.6+Sun/3.7W-hitachi-ul) id h9H8NGY09035; Fri, 17 Oct 2003 17:23:16 +0900 (JST) Received: from hul2.hitachi-ul.co.jp [158.211.18.118] by hul3.hitachi-ul.co.jp with SMTP id TAA09034 ; Fri, 17 Oct 2003 17:23:16 +0900 Received: from k5jk-ux-09.hitachi-ul.co.jp (localhost [127.0.0.1]) by hul2.hitachi-ul.co.jp (8.8.8+Sun/3.6W-hul2) with ESMTP id RAA12727 for ; Fri, 17 Oct 2003 17:23:58 +0900 (JST) Received: from hitachi-ul.co.jp ([202.19.63.88]) by k5jk-ux-09.hitachi-ul.co.jp (8.11.4/8.11.4) with ESMTP id h9H8Nwu13758 for ; Fri, 17 Oct 2003 17:23:58 +0900 (JST) Message-ID: <3F8FA71D.3CB85976)at(hitachi-ul.co.jp> Date: Fri, 17 Oct 2003 17:24:16 +0900 From: "k.watanabe" X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: ja,en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: Application for calculating pocket volume for ligand Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers. Isn't application which calculates volume of protein pocket for ligand some known? I will wish free ware, if it can do. I need your help well. K. Watanabe Hitachi ULSI systems.