From chemistry-request@server.ccl.net Thu Dec 3 03:00:54 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA31942 for ; Thu, 3 Dec 1998 03:00:54 -0500 Received: from cacr.ioc.ac.ru (cacr.ioc.ac.ru [193.233.3.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA26533 Thu, 3 Dec 1998 02:56:49 -0500 (EST) Received: from cacr.ioc.ac.ru (nmr-v [193.233.3.213]) by cacr.ioc.ac.ru (8.8.8/EM.SRV.10.8) with ESMTP id KAA25229 for ; Thu, 3 Dec 1998 10:57:02 +0300 (MSK) Message-ID: <3666DFFC.2912F04D@cacr.ioc.ac.ru> Date: Thu, 03 Dec 1998 11:01:16 -0800 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.04 [en] (Win16; I) MIME-Version: 1.0 To: CCL_post Subject: rMD/NMR in Water Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, I am looking for Molecular Dynamics package for restrained MD simulations of DNA molecules using NMR-derived distance and angle restrains "in water solution". The following features are of most importance: 1) AMBER, CHARMM or equal on quality force field, 2) the ability to include water molecules and ions explicitly, 3) particle mesh Ewald method. Of course tools to set up water box and put ions, as well as parallel code, are very appreciated. The program must be freeware (please no low cost academic licenses). Undoubtedly, there are a lot of sites on the net listing all available MD software, but it would be better to get more exact solution rather than just a point to "MD-links" www page. The summary will follow. Thanks in advance! sincerely yours, Valentin. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Thu Dec 3 06:24:11 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA32088 for ; Thu, 3 Dec 1998 06:24:11 -0500 Received: from sirio.cineca.it (sirio.cineca.it [193.204.121.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA27531 Thu, 3 Dec 1998 06:20:02 -0500 (EST) Received: (from incci000@localhost) by sirio.cineca.it (8.8.5/8.7) id MAA01057; Thu, 3 Dec 1998 12:16:23 +0100 (MET) Date: Thu, 3 Dec 1998 12:16:22 +0100 (MET) From: Sigismondo Boschi To: Guido Germano cc: Computational Chemistry List Subject: Re: CCL:G:g94: shmget failed on SGI O2000 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Guido, do you remember me? I have compiled g94 (e2) on an SGI origin2000 (IRIX 6.4) and I can report my personal experience with it. g94 uses "system V shared memory" (shmget) for allocating the main pool memory on the origin, in order all the processors can use it. In the beginning I found that the jobs I could run was very small with respect the memory Origin installed here at CINECA: 16CPUs with a total of 8GB. After all I have found that the "maximum segment" allocable is a parameter of the kernel, set to 512MB by default (if I remember right). Its maximum value is instead 1/4 of the toatal memory, 2GB for our machine (256MWords). After the system manager have changed this parameter, I was able to run problems up to 250MWords of in-core memory. The name of the adjusted kernel parameter is "shmmax" and it is one of the "IPC parameters". If you have the same problem, I think you need to change it and recompile the kernel. I hope it helps. Bye! Sigismondo --------------------------------------- --------------------------------- |Sigismondo Boschi |tel: +39 51 6171559 | |CINECA (Gruppo Supercalcolo) - INSTM |fax: +39 51 6132198 | |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | |40033 Casalecchio di Reno (Bologna) | | |ITALY | | --------------------------------------- --------------------------------- On Wed, 2 Dec 1998, Guido Germano wrote: > Two days ago I compiled g94 D4 on a SGI Origin 2000 running IRIX 6.5.1. > The same geometry optimizations that run fine on an IBM core dump after > two steps in l301 with "shmget failed" as the last line of the output > file. If restarted from the chk, they do other two steps, then core dump > again, and so on. I have "unlimit" in my .login before I source > g94.login. Increasing %mem is no help (the default of 4000000 words is > enough anyway). The Origin has 8 processors with 1 GB of RAM. > > I searched the CCL archives and found the same question being asked > about g92, but no answer. So far no answer from help@gaussian either. > > Guido Germano > > University of Bristol, +44-117-928 9000 ext. 8755 > http://www.phy.bris.ac.uk/staff/germano_g.html > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: g.germano@bristol.ac.uk > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From quest@ster.ccl.net Fri Nov 27 12:50:11 1998 Return-Path: Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA02626 for ; Fri, 27 Nov 1998 12:50:10 -0500 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA24302 Fri, 27 Nov 1998 12:47:22 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L103.Farlep.Net [208.244.49.229]) by Sun.Farlep.Net (8.9.1/8.9.0/Farlep-Mail-2.0) with ESMTP id TAA20289; Fri, 27 Nov 1998 19:46:54 +0200 (EET) Message-ID: <365EE2CE.92927113@farlep.net> Date: Fri, 27 Nov 1998 19:35:10 +0200 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: "jkl@ccl.net" , "istry@inster.ccl.net" Subject: Thanks References: <35E7E771.DFDB1B56@farlep.net> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Status: R Hello. I'd like to liquidate my subscribtion for the conference for a certain time. Thank you very much for cooperation. Alexander Herega From quest@ster.ccl.net Fri Nov 27 12:50:11 1998 Return-Path: Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA02626 for ; Fri, 27 Nov 1998 12:50:10 -0500 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA24302 Fri, 27 Nov 1998 12:47:22 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L103.Farlep.Net [208.244.49.229]) by Sun.Farlep.Net (8.9.1/8.9.0/Farlep-Mail-2.0) with ESMTP id TAA20289; Fri, 27 Nov 1998 19:46:54 +0200 (EET) Message-ID: <365EE2CE.92927113@farlep.net> Date: Fri, 27 Nov 1998 19:35:10 +0200 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: "jkl@ccl.net" , "istry@inster.ccl.net" Subject: Thanks Cc: kjj ljlj , "kjhk lkj" , ll@ll.ll.ll References: <35E7E771.DFDB1B56@farlep.net> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Status: R Hello. I'd like to liquidate my subscribtion for the conference for a certain time. Thank you very much for cooperation. Alexander Herega From quest@ster.ccl.net Fri Nov 27 12:50:11 1998 Return-Path: Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA02626 for ; Fri, 27 Nov 1998 12:50:10 -0500 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA24302 Fri, 27 Nov 1998 12:47:22 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L103.Farlep.Net [208.244.49.229]) by Sun.Farlep.Net (8.9.1/8.9.0/Farlep-Mail-2.0) with ESMTP id TAA20289; Fri, 27 Nov 1998 19:46:54 +0200 (EET) Message-ID: <365EE2CE.92927113@farlep.net> Date: Fri, 27 Nov 1998 19:35:10 +0200 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: "jkl@ccl.net" , "istry@inster.ccl.net" Subject: Thanks Cc: kjj ljlj , "kjhk lkj" , ll@ll.ll.ll References: <35E7E771.DFDB1B56@farlep.net> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Status: R Hello. I'd like to liquidate my subscribtion for the conference for a certain time. Thank you very much for cooperation. Alexander Herega From quest@ster.ccl.net Fri Nov 27 12:50:11 1998 Return-Path: Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA02626 for ; Fri, 27 Nov 1998 12:50:10 -0500 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA24302 Fri, 27 Nov 1998 12:47:22 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L103.Farlep.Net [208.244.49.229]) by Sun.Farlep.Net (8.9.1/8.9.0/Farlep-Mail-2.0) with ESMTP id TAA20289; Fri, 27 Nov 1998 19:46:54 +0200 (EET) Message-ID: <365EE2CE.92927113@farlep.net> Date: Fri, 27 Nov 1998 19:35:10 +0200 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: "jkl@ccl.net" , "istry@inster.ccl.net" Subject: Thanks Cc: kjj ljlj , "kjhk lkj" , ll@ll.ll.ll References: <35E7E771.DFDB1B56@farlep.net> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Status: R Hello. I'd like to liquidate my subscribtion for the conference for a certain time. Thank you very much for cooperation. Alexander Herega From quest@ster.ccl.net Fri Nov 27 12:50:11 1998 Return-Path: Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA02626 for ; Fri, 27 Nov 1998 12:50:10 -0500 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA24302 Fri, 27 Nov 1998 12:47:22 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L103.Farlep.Net [208.244.49.229]) by Sun.Farlep.Net (8.9.1/8.9.0/Farlep-Mail-2.0) with ESMTP id TAA20289; Fri, 27 Nov 1998 19:46:54 +0200 (EET) Message-ID: <365EE2CE.92927113@farlep.net> Date: Fri, 27 Nov 1998 19:35:10 +0200 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: "jkl@ccl.net" , "istry@inster.ccl.net" Subject: Thanks Cc: kjj ljlj , "kjhk lkj" , ll@ll.ll.ll References: <35E7E771.DFDB1B56@farlep.net> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Status: R Hello. I'd like to liquidate my subscribtion for the conference for a certain time. Thank you very much for cooperation. Alexander Herega From quest@ster.ccl.net Fri Nov 27 12:50:11 1998 Return-Path: Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA02626 for ; Fri, 27 Nov 1998 12:50:10 -0500 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA24302 Fri, 27 Nov 1998 12:47:22 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L103.Farlep.Net [208.244.49.229]) by Sun.Farlep.Net (8.9.1/8.9.0/Farlep-Mail-2.0) with ESMTP id TAA20289; Fri, 27 Nov 1998 19:46:54 +0200 (EET) Message-ID: <365EE2CE.92927113@farlep.net> Date: Fri, 27 Nov 1998 19:35:10 +0200 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: "jkl@ccl.net" , "istry@inster.ccl.net" Subject: Thanks Cc: kjj ljlj , "kjhk lkj" , ll@ll.ll.ll References: <35E7E771.DFDB1B56@farlep.net> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Status: R Hello. I'd like to liquidate my subscribtion for the conference for a certain time. Thank you very much for cooperation. Alexander Herega From chemistry-request@server.ccl.net Thu Dec 3 15:03:22 1998 Received: from cis.ohio-state.edu (mail.cis.ohio-state.edu [164.107.115.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00235 for ; Thu, 3 Dec 1998 15:03:21 -0500 Received: from hammond.cis.ohio-state.edu (xue@hammond.cis.ohio-state.edu [164.107.17.6]) by cis.ohio-state.edu (8.9.1/8.9.1) with ESMTP id OAA02078 for ; Thu, 3 Dec 1998 14:59:14 -0500 (EST) From: jing xue Received: (xue@localhost) by hammond.cis.ohio-state.edu (8.8.0/8.6.4) id OAA25200 for chemistry@server.ccl.net; Thu, 3 Dec 1998 14:59:12 -0500 (EST) Date: Thu, 3 Dec 1998 14:59:12 -0500 (EST) Message-Id: <199812031959.OAA25200@hammond.cis.ohio-state.edu> To: chemistry@server.ccl.net Subject: test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1 test forwarder.new from cis 3.1