From chemistry-request@ccl.net Sat Mar 5 04:25:14 2005 Received: from marge.uochb.cas.cz (marge.uochb.cas.cz [147.231.129.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j259PDE2007113 for ; Sat, 5 Mar 2005 04:25:13 -0500 Received: by marge.uochb.cas.cz (Postfix, from userid 8) id 5DCD77AB9; Sat, 5 Mar 2005 10:25:12 +0100 (CET) Received: from [147.231.129.82] (teo082.uochb.cas.cz [147.231.129.82]) by marge.uochb.cas.cz (Postfix) with ESMTP id 87CF37A09; Sat, 5 Mar 2005 10:25:11 +0100 (CET) Message-ID: <42297AF4.1030401=at=uochb.cas.cz> Date: Sat, 05 Mar 2005 10:25:08 +0100 From: "Mgr. Lubos Vrbka" Reply-To: lubos.vrbka=at=uochb.cas.cz Organization: IOCB User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: forli=at=unisi.it Cc: chemistry=at=ccl.net Subject: Re: CCL:addiong ions to simulation box References: <01LLHVFO59AQ99EOLE=at=mailsrv.unisi.it> In-Reply-To: <01LLHVFO59AQ99EOLE=at=mailsrv.unisi.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 hi stefano, thank you for your hint with gromacs... however it seems that it is seriously broken in this respect. see, e.g. http://www.gromacs.org/pipermail/gmx-users/2004-August/011925.html i always encounter the same problem - when larger amount of molecules is being added to simulation box with protein, genbox starts placing the molecules inside the protein structure... it's a pity, since this is exactly the functionality i need... :( if you have any other suggestions, please let me know. regards, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic ..................................................... From chemistry-request@ccl.net Sat Mar 5 06:19:09 2005 Received: from av7-1-sn4.m-sp.skanova.net (av7-1-sn4.m-sp.skanova.net [81.228.10.110]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j25BJ7E2011856 for ; Sat, 5 Mar 2005 06:19:07 -0500 Received: by av7-1-sn4.m-sp.skanova.net (Postfix, from userid 502) id 28B5037E4F; Sat, 5 Mar 2005 11:20:01 +0100 (CET) Received: from smtp2-1-sn4.m-sp.skanova.net (smtp2-1-sn4.m-sp.skanova.net [81.228.10.183]) by av7-1-sn4.m-sp.skanova.net (Postfix) with ESMTP id 1879637E4A; Sat, 5 Mar 2005 11:20:01 +0100 (CET) Received: from [192.168.0.98] (h19n2fls33o1006.telia.com [217.209.70.19]) by smtp2-1-sn4.m-sp.skanova.net (Postfix) with ESMTP id CF3EE37E53; Sat, 5 Mar 2005 11:20:00 +0100 (CET) Message-ID: <422987D0.9000303*at*htu.se> Date: Sat, 05 Mar 2005 11:20:00 +0100 From: Steven Kirk User-Agent: Mozilla Thunderbird 1.0 (X11/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry*at*ccl.net Cc: "'Narasinga Rao'" Subject: CCL:Sharing files between Linix and Windows partitions References: <20050304165336.C265815C6A*at*mta-1.mail.nethere.net> In-Reply-To: <20050304165336.C265815C6A*at*mta-1.mail.nethere.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Ross Walker wrote: > Dear Narasinga, >>I would like to find out if it is possible to share files >>between Windows >>and Linux partitions on the same system? For example, is >>there a way to >>launch a browser(say, IE) in the Windows partition and have >>it run off the >>Apachee web server running on the Linux partition of that system? Narasinga, do you mean that Windows and Linux should be *running* simultaneously ? If so, you will need some kind of 'virtualization' software, e.g. VMware , to let you run the two different operating systems simultaneously on the same machine. By the way, the Apache webserver software is also available for Windows. By storing the webpages on a filesystem readable to both Windows and Linux (see below), the webserver could be configured to be functionally identical regardless of what operating system you are running. > Linux can mount windows partitions on standard mount points although the > support will depend on your kernel version and/or what is compiled in. NTFS > partitions can be mounted read only, you can also mount them as read write > but this is dangerous. Yes, you need to make sure that you have a kernel module installed to handle NTFS file systems. Take a look here: http://linux-ntfs.sourceforge.net/ An alternative route is to use Captive-NTFS (http://www.jankratochvil.net/project/captive/) This relies on Linux finding and reusing the native *Windows* NTFS driver files, so this might work well on a Linux-Windows dual-boot system. This technique claims to allow full read/write access to NTFS partitions, but I haven't personally tested it. I have seen reports that Windows XP SP2 breaks Captive-NTFS, but apparently there is a way around this (http://www.oreillynet.com/pub/wlg/6261). Of course, if you set up a Windows FAT32 filesystem somewhere on your machine, both Linux and Windows will be able to read and write to it. > > For Windows you can use a program called Explore2fs > http://uranus.it.swin.edu.au/~jn/linux/explore2fs.htm which allows you to > read Ext2 (and I believe Ext3, since it should be backwards compatible with > Ext2) file systems under windows. Seconded - very useful program ! [snipped] -- Dr. Steven R. Kirk Dept. of Computer Science, TMD http://taconet.webhop.org Univ. of Trollhattan/Uddevalla Ph: +46 520 475318 Fax:+46 520 475399 P.O. Box 957 Trollhattan 461 29 SWEDEN From chemistry-request@ccl.net Sat Mar 5 07:03:11 2005 Received: from av9-2-sn1.fre.skanova.net (av9-2-sn1.fre.skanova.net [81.228.11.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j25C37E2013955 for ; Sat, 5 Mar 2005 07:03:07 -0500 Received: by av9-2-sn1.fre.skanova.net (Postfix, from userid 502) id 68DCA37E63; Sat, 5 Mar 2005 11:59:44 +0100 (CET) Received: from smtp3-2-sn1.fre.skanova.net (smtp3-2-sn1.fre.skanova.net [81.228.11.164]) by av9-2-sn1.fre.skanova.net (Postfix) with ESMTP id 5990D37E5B; Sat, 5 Mar 2005 11:59:44 +0100 (CET) Received: from 192.168.0.101 (h88n2fls34o1123.telia.com [81.224.175.88]) by smtp3-2-sn1.fre.skanova.net (Postfix) with ESMTP id EC99737E4A; Sat, 5 Mar 2005 11:59:43 +0100 (CET) Subject: Re: CCL:addiong ions to simulation box From: David van der Spoel To: "Mgr. Lubos Vrbka" Cc: forli :: unisi.it, chemistry :: ccl.net In-Reply-To: <42297AF4.1030401 :: uochb.cas.cz> References: <01LLHVFO59AQ99EOLE :: mailsrv.unisi.it> <42297AF4.1030401 :: uochb.cas.cz> Content-Type: text/plain Date: Sat, 05 Mar 2005 11:53:50 +0100 Message-Id: <1110020030.5759.8.camel@vangogh> Mime-Version: 1.0 X-Mailer: Evolution 2.0.2 (2.0.2-3) Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.4 required=7.5 tests=RM_fw_FromIsPhras2,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Sat, 2005-03-05 at 10:25 +0100, Mgr. Lubos Vrbka wrote: > hi stefano, > > thank you for your hint with gromacs... however it seems that it is > seriously broken in this respect. see, e.g. > http://www.gromacs.org/pipermail/gmx-users/2004-August/011925.html > i always encounter the same problem - when larger amount of molecules is > being added to simulation box with protein, genbox starts placing the > molecules inside the protein structure... it's a pity, since this is > exactly the functionality i need... :( The example in the mailing list is quite extreme in the sense that they try to add 2400 molecules to a 4 x 4 x 4 nm box. I'm not sure how broken it is. An alternative is to solvate a protein in a mixed solvent (using genbox) or simply build a box with lots of space between molecules and then use pressure scaling MD to compress the box. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel :: xray.bmc.uu.se spoel :: gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel :: xray.bmc.uu.se spoel :: gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@ccl.net Sat Mar 5 08:08:19 2005 Received: from cuces2.unisi.it (cuces2.unisi.it [193.205.4.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j25D8IE2016429 for ; Sat, 5 Mar 2005 08:08:18 -0500 Received: from mailsrv.unisi.it by mailsrv.unisi.it (PMDF V6.2-X17 #30893) id <01LLJ9BGQJE899EY3R * mailsrv.unisi.it> for chemistry * ccl.net; Sat, 05 Mar 2005 14:09:01 +0200 (MET-DST) Date: Sat, 05 Mar 2005 14:09:01 +0200 (MET-DST) From: forli * unisi.it Subject: RE: CCL:addiong ions to simulation box To: spoel * xray.bmc.uu.se, lubos.vrbka * uochb.cas.cz Cc: chemistry * ccl.net Message-id: <01LLJ9BGQJEA99EY3R * mailsrv.unisi.it> X-yahMAIL: YAHMAIL AXP-1.8.0 (MIME) (PMDF) (CGILIB AXP-1.6.12/OBJ) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net hi, Lubos, > i always encounter the same problem - when larger amount of molecules is > being added to simulation box with protein, genbox starts placing the > molecules inside the protein structure... how you can easily imagine, number of molecules and volume of the box are essential, because apparently the first parameter drive the placement of solvent in to the box. I agree with David, the algorithm is not perfect, of course, so using large box with a lot of mols, it can fails, but fine tuning parameters leads me to really good results. I don't yet tryed the pressure gradient, but I think it's an elegant way to test as soon as possible Stefano -- *********************************** Stefano Forli Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 e-mail: forli * unisi.it *********************************** From chemistry-request@ccl.net Sat Mar 5 12:54:32 2005 Received: from mserv.itpa.lt (mserv.itpa.lt [193.219.53.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j25HsVE2027861 for ; Sat, 5 Mar 2005 12:54:31 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.11/8.12.11) with ESMTP id j25H2K1n052453; Sat, 5 Mar 2005 19:02:20 +0200 (EET) (envelope-from tamulis.-at-.mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.11/8.12.11/Submit) with ESMTP id j25H2KSa052450; Sat, 5 Mar 2005 19:02:20 +0200 (EET) (envelope-from tamulis.-at-.mserv.itpa.lt) Date: Sat, 5 Mar 2005 19:02:20 +0200 (EET) From: Arvydas Tamulis To: "Mgr. Lubos Vrbka" cc: chemistry.-at-.ccl.net Subject: Re: CCL:addiong ions to simulation box In-Reply-To: <42283D3E.7050509.-at-.uochb.cas.cz> Message-ID: <20050305185806.G51595.-at-.mserv.itpa.lt> References: <42283D3E.7050509.-at-.uochb.cas.cz> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello Mgr. Lubos Vrbka, We put many water and lipid molecules surrounding PNA+Sensitizer::LipidPrecursor self-assembling system by using Molden software and later doing PM3 geometry optimization using G03 or GAMESS packages. Regards, Arvydas Tamulis On Fri, 4 Mar 2005, Mgr. Lubos Vrbka wrote: > Hello everybody: > > Is anyone aware of software allowing replacing waters in the simulations cell > (protein + water box) by small molecules? "Automatic" solution is preferred, > since I need to put many molecules to the solution. > > Any help is highly appreciated. With best regards, > Lubos > > -- >> ..................................................... > Mgr. Lubos Vrbka > > Center for Biomolecules and Complex Molecular Systems > Institute of Organic Chemistry and Biochemistry > Academy of Sciences of the Czech Republic > Prague, Czech Republic >> ..................................................... > > -= 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, jlabanow.-at-.nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > >