From owner-chemistry@ccl.net Fri Mar 16 07:27:00 2012 From: "pipek[a]gmx.net" To: CCL Subject: CCL:G: PBC calculations Message-Id: <-46511-120316072329-16516-lDls7mi3bYSeIK4EXavV2A..server.ccl.net> X-Original-From: pipek[]gmx.net Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 16 Mar 2012 12:23:20 +0100 MIME-Version: 1.0 Sent to CCL by: pipek/a\gmx.net Hallo Dr. Chaban, thanks for the reply. Up to now I use the Gaussian k point default. I dont have any experience with PBC calculations. The k mesh is the size of the unit cell and the number of k points the numbers of repetitions, right? Does your question imply I should reduce the number of k points? Thanks in advance, Anja -------- Original-Nachricht -------- > Datum: Wed, 14 Mar 2012 15:02:45 -0400 > Von: "Dr. Vitaly V. Chaban vvchaban _ gmail.com" > An: "Jatsch, Anja " > Betreff: CCL:G: PBC calculations > > Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban~~gmail.com] > Do you use any k-mesh? > > > Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. > Univ. Rochester, Rochester, New York 14627-0216 > THE UNITED STATES OF AMERICA > > > > > On Wed, Mar 14, 2012 at 5:06 AM, Anja Jatsch pipek..gmx.net > wrote: > > > > Sent to CCL by: "Anja  Jatsch" [pipek:+:gmx.net] > > Dear ccl users, > > > > I am trying to set up a PBC calculation on a measured crystal structure > (organic), but I always end up with the same error in the MO guess: > > > > Dimensions of /B2/ exceeded in AtP2B2. > > Error termination via Lnk1e in c:\program files\G09W\l401.exe > > > > I am using #p pbepbe/3-21g/auto and I really dont have a clue whats the > problem. There are almost 200 atoms in the unit cell, maybe its to large? > But Gaussian doesnt complain about the memory > > > > Thanks a lot for any idears! > > > > Anja>      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> > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From owner-chemistry@ccl.net Fri Mar 16 09:59:00 2012 From: "Dr. Vitaly V. Chaban vvchaban%%gmail.com" To: CCL Subject: CCL:G: PBC calculations Message-Id: <-46512-120316090428-2851-pkh4Q+TsxFUo46uGSni0Zw**server.ccl.net> X-Original-From: "Dr. Vitaly V. Chaban" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 16 Mar 2012 09:03:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban^^^gmail.com] K-meshes improve your sampling, but this is not simply the repetition of your unit cell. You may be able to find some clearer explanations on the web. Try "GammaOnly" option. I do not guarantee that will solve your particular error, though. In general, Gaussian has imperfect reputation as a tool for studying periodic structures, so it may be worthwhile to switch to eventually some plane-waves code. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Fri, Mar 16, 2012 at 7:23 AM, pipek[a]gmx.net wrote: > > Sent to CCL by: pipek/a\gmx.net > Hallo Dr. Chaban, > > thanks for the reply. Up to now I use the Gaussian k point default. I dont have any experience with PBC calculations. The k mesh is the size of the unit cell and the number of k points the numbers of repetitions, right? > > Does your question imply I should reduce the number of k points? > > Thanks in advance, > > Anja > > -------- Original-Nachricht -------- >> Datum: Wed, 14 Mar 2012 15:02:45 -0400 >> Von: "Dr. Vitaly V. Chaban vvchaban _ gmail.com" >> An: "Jatsch, Anja " >> Betreff: CCL:G: PBC calculations > >> >> Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban~~gmail.com] >> Do you use any k-mesh? >> >> >> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. >> Univ. Rochester, Rochester, New York 14627-0216 >> THE UNITED STATES OF AMERICA >> >> >> >> >> On Wed, Mar 14, 2012 at 5:06 AM, Anja Jatsch pipek..gmx.net >> wrote: >> > >> > Sent to CCL by: "Anja  Jatsch" [pipek:+:gmx.net] >> > Dear ccl users, >> > >> > I am trying to set up a PBC calculation on a measured crystal structure >> (organic), but I always end up with the same error in the MO guess: >> > >> > Dimensions of /B2/ exceeded in AtP2B2. >> > Error termination via Lnk1e in c:\program files\G09W\l401.exe >> > >> > I am using #p pbepbe/3-21g/auto and I really dont have a clue whats the >> problem. There are almost 200 atoms in the unit cell, maybe its to large? >> But Gaussian doesnt complain about the memory >> > >> > Thanks a lot for any idears! >> > >> > Anja>      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> >> > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a>      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 Fri Mar 16 13:44:00 2012 From: "Oleg Trott trott++scripps.edu" To: CCL Subject: CCL: ANN: Run AutoDock Vina on the World Community Grid Message-Id: <-46513-120316134157-4401-JkI5W/9e/6ZUphwi+h4iZg(_)server.ccl.net> X-Original-From: Oleg Trott Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 16 Mar 2012 10:11:42 -0700 MIME-Version: 1.0 Sent to CCL by: Oleg Trott [trott===scripps.edu] This should have been announced earlier, but better late than never: Qualified projects can now run AutoDock Vina calculations for free on the massively parallel World Community Grid. Existing projects using AutoDock Vina there include those targeting Malaria, Leishmaniasis and Schistosomiasis. Some of these projects average over 50 years worth of computation per day. Many thanks to the developers at IBM who made this possible, and to all of the volunteers who donate their idle CPU time! [1] AutoDock Vina: http://vina.scripps.edu [2] World Community Grid: http://www.worldcommunitygrid.org -- Oleg Trott, Ph.D. (Columbia University) Staff Scientist in the Olson Lab The Scripps Research Institute http://olegtrott.com