From chemistry-request@server.ccl.net Fri Aug 10 08:41:09 2001 Received: from zimail1.unizh.ch ([130.60.128.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7ACf8v08962 for ; Fri, 10 Aug 2001 08:41:08 -0400 Received: from rt ([130.60.152.83]) by zimail1.unizh.ch (8.9.3/8.9.3/10) with SMTP id OAA02490 for ; Fri, 10 Aug 2001 14:41:07 +0200 (MEST) Message-Id: <3.0.5.32.20010810143851.00a08480@rzu-mailhost.unizh.ch> X-Sender: rzusuntk.unizh.ch:spingler@rzu-mailhost.unizh.ch X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Fri, 10 Aug 2001 14:38:51 +0200 To: chemistry@ccl.net From: Bernhard Spingler Subject: Autodock 3.0.5 Linux awk Problem Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi all, The question has already been asked in the newsgroup in March, but the suggested solution did not help in my case: >> I have a question about the script "mol2topdbq" that comes with >> AutoDock 3.0.5. I changed the "nawk" in the very beginning to the >> awk-version I'm using on my PC (Suse Linux 7.1) "gawk", but this scripts >> does not work properly - upon exeution, I get the following message: >> >> gawk: cmd. line:33: fatal: expression for `<' redirection has null string >> value >Try changing "nawk" to "gawk --traditional" and see if that helps. We have a PC running Linux Suse 6.4 i386, and I tried to change to gawk, awk, "gawk --traditional", or "awk --traditional", neither of them did help. Thanks a lot for any suggestions Best regards Bernhard Spingler From chemistry-request@server.ccl.net Fri Aug 10 02:07:37 2001 Received: from hkusua.hku.hk ([147.8.2.91]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7A67av16971 for ; Fri, 10 Aug 2001 02:07:36 -0400 Received: from win95pc ([147.8.148.66]) by hkusua.hku.hk (8.11.4/8.11.4) with SMTP id f7A68aH14107 for ; Fri, 10 Aug 2001 14:08:36 +0800 (HKT) Message-ID: <003401c12162$e5668f60$42940893@win95pc.hku.hk> From: "dwang" To: Subject: Problem on memory. Date: Fri, 10 Aug 2001 14:08:37 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0031_01C121A5.F35774C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0031_01C121A5.F35774C0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear cclers, I just bought a pc with p4 1.7G, 1G memory, asus mainboard(in the manual = it can support memory up to 2G). OS is windows98. When i run Gaussian98, = I can't set the memory distributed to G98 more than 250MB, and if I = start the Norton Antivirous real-time scan, i can't run ms-dos because = of low memory(information on the computer) but I think that no more than = 500MB memory is used at the time. Where is the rest memory? If i remove = 500MB memory, everything goes ok except that I still can't set the = memory to G98 more than 250MB. Why??? Is it because of G98 or Win98? Any = advices will be appreciated. Wang Dongqi Dept. of Chemistry Univ. of HongKong Pokfulam Road HongKong Tel: (852)28598947 ------=_NextPart_000_0031_01C121A5.F35774C0 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear = cclers,
I just = bought a pc with p4 1.7G, 1G=20 memory, asus mainboard(in the manual it can support memory up to 2G). OS = is=20 windows98. When i run Gaussian98, I can't set the memory distributed to = G98 more=20 than 250MB, and if I start the Norton Antivirous real-time scan, i can't = run=20 ms-dos because of low memory(information on the computer) but I think = that no=20 more than 500MB memory is used at the time. Where is the rest memory? If = i=20 remove 500MB memory, everything goes ok except that I still can't set = the memory=20 to G98 more than 250MB. Why??? Is it because of G98 or Win98? Any = advices will=20 be appreciated.
 
Wang = Dongqi
Dept. of=20 Chemistry
Univ. of HongKong
Pokfulam Road
HongKong
Tel:=20 (852)28598947
------=_NextPart_000_0031_01C121A5.F35774C0-- From chemistry-request@server.ccl.net Thu Aug 9 22:29:52 2001 Received: from hotmail.com ([64.4.37.168]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7A2Tqv09842 for ; Thu, 9 Aug 2001 22:29:52 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 9 Aug 2001 19:29:47 -0700 Received: from 133.11.92.210 by pv2fd.pav2.hotmail.msn.com with HTTP; Fri, 10 Aug 2001 02:29:46 GMT X-Originating-IP: [133.11.92.210] From: "tianxiao young" To: chemistry@ccl.net Subject: ESP charge in ADF Date: Fri, 10 Aug 2001 02:29:46 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 10 Aug 2001 02:29:47.0231 (UTC) FILETIME=[52B71EF0:01C12144] Dear CCLers, Does anyone know how to calculate the ESP or CHelpG charge using ADF program? Because the Mulliken charge seems to be underestimating the polarization in the actinide complexes, I need to use the ESP or CHelpG charge. Your response will be greatly appreciated. Thank you very much in advance. Tianxiao Yang _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Fri Aug 10 06:41:18 2001 Received: from relay1.post.cz ([195.250.146.12]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7AAfHv05908 for ; Fri, 10 Aug 2001 06:41:17 -0400 Received: from smtp1.post.cz (smtp1.post.cz [195.250.146.13]) by relay1.post.cz (8.11.3/8.11.2) with ESMTP id f7AAFKh49084 for ; Fri, 10 Aug 2001 12:15:20 +0200 (CEST) (envelope-from sasha1@post.cz) Received: (from root@localhost) by smtp1.post.cz (8.11.2/8.11.2/Debian 8.11.2-1) id f7AAEgU26423; Fri, 10 Aug 2001 12:14:42 +0200 From: sasha1@post.cz X-Priority: 1 MIME-Version: 1.0 Message-Id: <3B73B412.000001.26412@smtp1> Date: Fri, 10 Aug 2001 12:14:37 +0200 (CEST) Content-Type: Text/Plain Content-Transfer-Encoding: 7bit To: chemistry@ccl.net Subject: A bit more on designing high-energy species Recently somebody asked the CCL list for some instructive computational illustrations for energy-rich compounds. Here is an additional interesting comment related to the topic: http://groups.yahoo.com/group/amadeus_sk/message/44 From chemistry-request@server.ccl.net Fri Aug 10 11:55:35 2001 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7AFtZv12150 for ; Fri, 10 Aug 2001 11:55:35 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id SAA15362; Fri, 10 Aug 2001 18:54:48 +0300 (EET DST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Fri, 10 Aug 2001 18:54:48 +0300 (EET DST) From: Mikael Johansson X-Sender: To: dwang cc: Subject: Re: CCL:Problem on memory. In-Reply-To: <003401c12162$e5668f60$42940893@win95pc.hku.hk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Wang and All! Windows 95/98/ME can not properly handle systems with more memory than 512MB. See http://support.microsoft.com/support/kb/articles/Q253/9/12.ASP You need Linux or Windows 2000. Have a nice day, Mikael J. On Fri, 10 Aug 2001, dwang wrote: > I just bought a pc with p4 1.7G, 1G memory, asus mainboard(in the > manual it can support memory up to 2G). OS is windows98. When i run > Gaussian98, I can't set the memory distributed to G98 more than 250MB, > and if I start the Norton Antivirous real-time scan, i can't run ms-dos > because of low memory(information on the computer) but I think that no > more than 500MB memory is used at the time. Where is the rest memory? If > i remove 500MB memory, everything goes ok except that I still can't set > the memory to G98 more than 250MB. Why??? Is it because of G98 or Win98? > Any advices will be appreciated. From chemistry-request@server.ccl.net Fri Aug 10 11:59:03 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7AFx2v12216 for ; Fri, 10 Aug 2001 11:59:03 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id RAA04218 ; Fri, 10 Aug 2001 17:58:49 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id RAA24441; Fri, 10 Aug 2001 17:59:13 +0200 Date: Fri, 10 Aug 2001 17:59:13 +0200 Message-Id: <200108101559.RAA24441@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: vani@reef.phys.lsu.edu CC: chemistry@ccl.net In-reply-to: (message from Vemparala Satyavani on Thu, 9 Aug 2001 10:32:20 -0500 (CDT)) Subject: Re: CCL:calculation of stress with SHAKE/RATTLE References: > how does one calculate the stresses when constraint dynamics is used? or > is there a way to seperate the constraint forces as two equal and opposite > forces so that the stress calculation is simple?(am using the RATTLE > routine provided in Allen & Tildesley book) If you have only pair distance constraints, then the constraint forces can be decomposed in such a way. In fact, just look at the derivation of SHAKE and RATTLE: the constraint forces are written as a Lagrange multiplier times the pair distance. The Lagrange multipliers can be calculated explicitly during the SHAKE/RATTLE iterations. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Aug 10 12:39:12 2001 Received: from ucontrol.mobiledns.com ([216.99.37.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7AGd8v12733 for ; Fri, 10 Aug 2001 12:39:11 -0400 Received: from MattLiLa (enterprise.divine.net [216.99.37.202] (may be forged)) by ucontrol.mobiledns.com (8.10.0.Beta6/8.10.0.Beta6) with SMTP id f7AFPsY01979; Fri, 10 Aug 2001 11:25:55 -0400 From: "Matt Foley" To: Cc: Subject: your motherboard dilemma Date: Fri, 10 Aug 2001 12:41:38 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Todd, I saw your post on Beowulf-Digest. I am curious on how you arrived at the ASUS A7S-VM and the Shuttle MS21N? If you would like, please call me and I'll put you together with one of our tech guys in an attempt to help. Linux Labs possesses an extremely high level of Linux HPC expertise. Members of our technical team have been working with the concept of parallel cluster supercomputing since the mid 1980s and long before the Linux/Beowulf movement started in 1994. We sell totally-integrated, turn-key, custom-specified, make-to-order systems as a primary hardware offering. And we also assist customers with a variety of hourly rate consulting-type services like kernel development & upgrades, code optimization, parallelization & porting, system upgrades and software development. We hope to work with you. Regards, Matt Matt Foley Sales Manager Linux Labs 230 Peachtree Street NW #701 Atlanta, GA 30303 404.577.7747 - main www.linuxlabs.com From chemistry-request@server.ccl.net Fri Aug 10 19:04:15 2001 Received: from georgetown.edu ([141.161.1.110]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7AN4Fv19233 for ; Fri, 10 Aug 2001 19:04:15 -0400 Received: from mailhost.georgetown.edu (mailhost.georgetown.edu [141.161.1.103]) by georgetown.edu (8.11.1/8.11.1) with ESMTP id f7AN4Ab13596 for ; Fri, 10 Aug 2001 19:04:10 -0400 (EDT) Received: from georgetown.edu (knauer.chemistry.georgetown.edu [141.161.37.20]) (authenticated as knauerc with PLAIN (0 bits)) by mailhost.georgetown.edu (8.11.1/8.11.1) with ESMTP id f7AN44k23138 (using TLSv1/SSLv3 with cipher RC4-MD5 (128 bits) verified NO) for ; Fri, 10 Aug 2001 19:04:09 -0400 (EDT) Message-ID: <3B7468D0.88E9AE64@georgetown.edu> Date: Fri, 10 Aug 2001 19:05:52 -0400 From: knauerc Organization: Georgetown University X-Mailer: Mozilla 4.75 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Monte Carlo simulations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone know of any available software for Monte Carlo simulations of adsorbed lattice gases, (Ising model), in the canonical ensemble and in the Gibbs ensemble? I'm interested in polar molecules adsorbed on polar surfaces, (orientation variable makes this a spin 1 system instead of spin 1/2), but anything would be helpful. Connie Knauer Graduate Student Georgetown University knauerc@georgetown.edu