From owner-chemistry@ccl.net Tue Mar 22 05:28:00 2011 From: "Daniel Jana dfjana^^gmail.com" To: CCL Subject: CCL:G: G09 in windows 7 Message-Id: <-44171-110322052650-29005-luM187MdJinC4imBWAUZWA-x-server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 Mar 2011 10:26:43 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana],[gmail.com] Hello Dario, I don't think you give us enough information, but G09W is compatible with Windows 7, as can be seen here: http://www.gaussian.com/g_prod/g09w.htm so compatibility shouldn't be the problem. Are you using a laptop? If so, the problem may be due to overheating. Try doing something else that is computationally intensive (running one of these Folding##Home type programs, for instance) and see if that takes your computer down. If you don't feel like "wasting" your cpu time, try creating a Virtual Machine (with VirtualBox for instance) and running either Windows XP or Linux in it. Then run Gaussian inside it. If that still crashes your real machine, then the problem is not on the interaction of Gaussian with your operating system. It may be due to overheating as already mentioned or, possibly, due to a issue with RAM. Best of luck, Daniel On 22 March 2011 00:35, Dario Fernando Coral ferchocoralg16 ~ gmail.com wrote: > > Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16###gmail.com] > Regards > > I have been running G09W in Windows 7. Lately, my machine has restarted during my calculates so, i suspect that is because G09W is not compatible with the operative system. However, i am not sure. > > If anyone knows the reason of this problem or have suggestions, please let me know. > > Thanks in advance. > > Dario Fernando Coral Obando > Chemistry Student > Universidad de Nario, Pasto, Colombia>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Mar 22 08:00:00 2011 From: "Francois Zielinski francois.zielinski**univ-rouen.fr" To: CCL Subject: CCL:G: G09 in windows 7 Message-Id: <-44172-110322064931-6088-w4tUXVfBNyCTL+PbHV8l4A!=!server.ccl.net> X-Original-From: Francois Zielinski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Tue, 22 Mar 2011 11:49:19 +0100 MIME-Version: 1.0 Sent to CCL by: Francois Zielinski [francois.zielinski]![univ-rouen.fr] Hello Dario, Here's a few tips in addition to Daniel analysis. To diagnose hardware failure, you may use those tools : * OCCT is a stress test, it will draw all the juice from your system to see if it can run stable in the worst conditions (running F[]H is a good test as well, and a great enterprise, but registering and getting the first runs might take you some time) http://www.ocbase.com/perestroika_en/index.php?Download * In order to distinguish power failure or overheating, you should monitor your CPU temperature with a soft like Hardware Monitor. I would not consider a CPU running over 70°C as reliable. http://www.cpuid.com/softwares/hwmonitor.html Good luck, best regards. François Quoting "Daniel Jana dfjana^^gmail.com" : > > Sent to CCL by: Daniel Jana [dfjana],[gmail.com] > Hello Dario, > > I don't think you give us enough information, but G09W is compatible > with Windows 7, as can be seen here: > http://www.gaussian.com/g_prod/g09w.htm > > so compatibility shouldn't be the problem. > Are you using a laptop? If so, the problem may be due to overheating. > Try doing something else that is computationally intensive (running > one of these Folding]-[Home type programs, for instance) and see if that > takes your computer down. If you don't feel like "wasting" your cpu > time, try creating a Virtual Machine (with VirtualBox for instance) > and running either Windows XP or Linux in it. Then run Gaussian inside > it. If that still crashes your real machine, then the problem is not > on the interaction of Gaussian with your operating system. It may be > due to overheating as already mentioned or, possibly, due to a issue > with RAM. > > Best of luck, > Daniel > > On 22 March 2011 00:35, Dario Fernando Coral ferchocoralg16 ~ > gmail.com wrote: >> >> Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16###gmail.com] >> Regards >> >> I have been running G09W in Windows 7. Lately, my machine has >> restarted during my calculates so, i suspect that is because G09W >> is not compatible with the operative system. However, i am not sure. >> >> If anyone knows the reason of this problem or have suggestions, >> please let me know. >> >> Thanks in advance. >> >> Dario Fernando Coral Obando >> Chemistry Student >> Universidad de Nario, Pasto, Colombia> > > From owner-chemistry@ccl.net Tue Mar 22 10:44:00 2011 From: "Roscioni O.M. omr===soton.ac.uk" To: CCL Subject: CCL: free software for nanoparticle building and visualizing Message-Id: <-44173-110322102941-14093-Czqsf6f/SsQTULyy08p/Mg!^!server.ccl.net> X-Original-From: "Roscioni O.M." Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Mar 2011 14:29:00 +0000 MIME-Version: 1.0 Sent to CCL by: "Roscioni O.M." [omr!^!soton.ac.uk] You can try GDIS (http://gdis.sourceforge.net). Although the program does not have any specific feature for building nanoparticles, you can follow these steps: 1) open the unit cell file of your bulk material 2) replicate the unit cell and make a supercell (something like 20x20x20) 3) carve the nanoparticle by hand. Quite a tedious task, though. In addition to point 3, I also recommend to switch between the CPK and Ball&Stick visualisations. The CPK is better suited to figure out the global shape of your cluster, while the B&S allows you to select accurately the atoms to be deleted. Hope that helps. Otello ________________________________________ > From: owner-chemistry+omr==soton.ac.uk:-:ccl.net [owner-chemistry+omr==soton.ac.uk:-:ccl.net] On Behalf Of M. Q Fatmi qaiser_fatmi**yahoo.com [owner-chemistry:-:ccl.net] Sent: 19 March 2011 20:50 To: Roscioni O.M. Subject: CCL: free software for nanoparticle building and visualizing Sent to CCL by: "M. Q Fatmi" [qaiser_fatmi()yahoo.com] Hi, Could anyone kindly tell me if there is any free software available to build and visualize nano-particles. Thanks in advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Mar 22 13:34:00 2011 From: "John Free johnfree198 a gmail.com" To: CCL Subject: CCL: Looking for a summer school or tutorial workshop in QM/MM Message-Id: <-44174-110322113640-20073-tMzFEfjrpd8pX5/cyyFrpg_+_server.ccl.net> X-Original-From: "John Free" Date: Tue, 22 Mar 2011 11:36:37 -0400 Sent to CCL by: "John Free" [johnfree198=-=gmail.com] Dear All, I am looking for a summer school or tutorial workshop about application of QM/MM in biological systems.If you know, Please kindly send me the link. Thanks in advance, John From owner-chemistry@ccl.net Tue Mar 22 14:09:00 2011 From: "Alessandro Curioni cur-,-zurich.ibm.com" To: CCL Subject: CCL: New CPMD release and web site Message-Id: <-44175-110322123117-29772-tusaEzvh5DVxCl4xeLN2Qg.:.server.ccl.net> X-Original-From: "Alessandro Curioni" Date: Tue, 22 Mar 2011 12:31:10 -0400 Sent to CCL by: "Alessandro Curioni" [cur++zurich.ibm.com] Dear Collegues, On behalf of the CPMD developer community I would like to announce the release of the version 3.15.1. This version comes out after 2 years from the last release. During this time frame the developer community has been working hard on improving, bug fixing and increasing the performance of the code on the latest available computing architectures. Several developers, have also implemented new algorithms respectively improving the existing ones. In details, CPMD version 3.15.1 brings (in parentheses major contributors): -) A new efficient Orthogonalization scheme (Costas Bekas and Alessandro Curioni) -) Constrained Density Functional Theory (Harald Oberhofer) -) Force Matching in QM/MM runs (Ivano Tavernelli) -) Generalized Langevin Thermostat (Michele Ceriotti) -) HSE06 (Hannu Komsa and Alfredo Pasquarello) -) Multiple Walkers in Metadynamics (Nisanth Nair) -) New configuration files for several new architectures (Mauro Boero, Alessandro Curioni) -) New extende pseudopotential library (Mauro Boero) -) Several bug fixes and improvements for scalability and performance (Almost every developer) -) Surface Hopping and Non-adiabatic Coupling Vectors withing TDDFT (Ivano Tavernelli) -) Ehrenfest Molecular Dynamics (Ivano Tavernelli) We would highly suggest you to download (see below for instructions) the latest version and report, in the future, possible issues and problems related to the 3.15.1 version only. Together with a new release, we are deploying a new website (many thanks to Teodoro Laino), which will provide an optimal platform to discuss issues and report problems. Compared to the old website, the new one offers a more dynamic environment: -) an issue tracker (to post issues and problems for the 3.15.1 release) -) a search engine screening through all the website information -) a bibliography manager offering for each article the DOI link to the paper -) Highlights: we would like on a monthly deadline to have on the main page outstanding research work performed with CPMD -) News and Events ( check in there for the CPMD 2011 conference) The mailing list has not been modified and will be always functional. The new website is available at the usual URL: http://www.cpmd.org and the new release can be downloaded from the URL: http://cpmd.org/download Just right-clicking on the package you want to download and save in your local folder. In order to download the software, you need to have a valid ID and password. Unfortunately the old password are not valid any longer, therefore we kindly invite you to apply for a new ID/password. The process is very simple, just follow the instruction on the URL: http://cpmd.org/download/cpmd-download-1/accept-license upon completion, you will receive in due time, the information to setup your favourite password. We hope you will enjoy both the new version of the CPMD code and the new CPMD website and wishing you millions of CPMD hours calculations we look forward to hear from you any feedback and/or comment. I would like to thank Teodoro Laino, Irina Fedulova and Costas Bekas without their precious contribution we would not have get to this new release/web site. Best Regards, Alessandro Curioni for the CPMD Team From owner-chemistry@ccl.net Tue Mar 22 22:43:00 2011 From: "Prof. J. Andrew McCammon jmccammon**mail.ucsd.edu" To: CCL Subject: CCL: [QSAR] Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Message-Id: <-44176-110322135752-10003-6sf86EDJXnJ6JI0ARq/now-$-server.ccl.net> X-Original-From: "Prof. J. Andrew McCammon" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Mar 2011 10:55:22 -0700 MIME-Version: 1.0 Sent to CCL by: "Prof. J. Andrew McCammon" [jmccammon=-=mail.ucsd.edu] David Shaw, our distinguished alumnus, will also present this talk on April 26 at UCSD: See http://mbtg.ucsd.edu/ The Shaw group's work is absolutely transformative. All are welcome. With best wishes, -- J. Andrew McCammon Investigator, Howard Hughes Medical Institute; Investigator, NSF Center for Theoretical Biological Physics; Joseph E. Mayer Professor of Theoretical Chemistry; Distinguished Professor of Pharmacology; University of California at San Diego; Fellow, San Diego Supercomputer Center; http://mccammon.ucsd.edu/ -----Original Message----- > From: qsar_society-bounces__ccl.net [mailto:qsar_society-bounces__ccl.net] On Behalf Of List for Members of Cheminformatics and QSAR Society Sent: Monday, March 21, 2011 12:45 PM To: comp-bio__magpie.bio.indiana.edu Cc: chemistry__ccl.net; qsar__ccl.net; Bio-soft__magpie.bio.indiana.edu; qsar__qsar.org Subject: [QSAR] Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Hi all, Here's an interesting topic I'd like your thoughts on - please pass along to your colleagues. Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Molecular dynamics simulation provides a potentially powerful tool for understanding the behavior of proteins at an atomic level of detail, but its relevance to drug design has been limited in part by the computational demands of such simulations. There's a specialized supercomputer, called Anton, that has simulated the behavior of a number of proteins for periods as long as a millisecond-approx. 100 times the length of the longest such simulations previously published - revealing pharmaceutically relevant aspects of protein dynamics that were previously inaccessible to both computational and experimental study. For further information, attend CHI's Structure-Based Drug Design conference on June 8-10, 2011 in Cambridge, MA. http://www.healthtech.com/sbd ************************* Jim Prudhomme Cambridge Healthtech Institute 781-972-5400 jprudhomme__healthtech.com -------------- next part -------------- An HTML attachment was scrubbed... URL: _______________________________________________ QSAR_Society mailing list QSAR_Society__qsar.org http://server.ccl.net/mailman/listinfo/qsar_society