From owner-chemistry@ccl.net Sat Sep 3 03:06:01 2011 From: "Partha Biswas partha361-x-gmail.com" To: CCL Subject: CCL:G: specify charge on atom in z-matrix Message-Id: <-45382-110903030432-32456-HaqvDQpPpv3sy7ku4IBF3Q ~~ server.ccl.net> X-Original-From: "Partha Biswas" Date: Sat, 3 Sep 2011 03:04:30 -0400 Sent to CCL by: "Partha Biswas" [partha361+*+gmail.com] Is it possible to specify charges on particular atoms instead of the whole molecule in the z-matrix to run calculation in Gaussian 03 or Gaussian 09 package? Please mention if any other package can handle this problem. Thanks in advance. From owner-chemistry@ccl.net Sat Sep 3 10:18:00 2011 From: "Johannes Hachmann jh*|*chemistry.harvard.edu" To: CCL Subject: CCL:G: specify charge on atom in z-matrix Message-Id: <-45383-110903091937-19581-/Qz+Uktv3h07QkbiwYlZ3g(~)server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 3 Sep 2011 09:19:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh(-)chemistry.harvard.edu] I don't think this is possible in g03 or g09, but you can use Constrained DFT in the Q-Chem package. However, you have to think very carefully about what you are doing and how formal charges may (or may not) translate to anything in a quantum chemical calculation! Best wishes Johannes ----------------------------------------------- Dr. Johannes Hachmann Postdoctoral Fellow Aspuru-Guzik Research Group Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 USA eMail: jh]=[chemistry.harvard.edu ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu]=[ccl.net [mailto:owner- > chemistry+jh388==cornell.edu]=[ccl.net] On Behalf Of Partha Biswas > partha361-x-gmail.com > Sent: Saturday, September 03, 2011 03:05 > To: Hachmann, Johannes > Subject: CCL:G: specify charge on atom in z-matrix > > > Sent to CCL by: "Partha Biswas" [partha361+*+gmail.com] > Is it possible to specify charges on particular atoms instead of the > whole molecule in the z-matrix to run calculation in Gaussian 03 or > Gaussian 09 package? Please mention if any other package can handle > this problem. > > Thanks in advance. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Sat Sep 3 10:52:00 2011 From: "Tasaka Tomo t.tasaka() gmail.com" To: CCL Subject: CCL: Freeware Amorphous Builder Message-Id: <-45384-110903103641-5706-1qTjoH9HG1/tn6GoA4Ur7Q ~ server.ccl.net> X-Original-From: Tasaka Tomo Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 3 Sep 2011 23:36:31 +0900 MIME-Version: 1.0 Sent to CCL by: Tasaka Tomo [t.tasaka|gmail.com] Hi Jussi, some time ago, I used the same procedure you advised. though I think it's not so bad basically, I have some question as to dependency on basis structure as an input of packmol. meanwhile, I have never tried WWW(Wooten, Weaire and Winer) or RMC(Reverse Monte Carlo) methods before. if you have any experience or information, please advise. especially, I'd like to know about WWW code.. Thank you, Tomo 2011/9/2 Jussi Lehtola jussi.lehtola/./helsinki.fi : > > Sent to CCL by: Jussi Lehtola [jussi.lehtola ~~ helsinki.fi] > On Fri, 2 Sep 2011 07:48:52 +0900 > "Tasaka Tomo t.tasaka(a)gmail.com" wrote: >> Sent to CCL by: Tasaka Tomo [t.tasaka . gmail.com] >> Hello, >> >> packmol is a useful tool to build an initial structure for such MD. >> however, it seems to unsuitable for amorphous solids(e.g. no PBC >> support). > > You can circumvent this deficiency by creating a slightly smaller box > with packmol. You'll probably have to cook'n'cool the structure anyway, > since the created packing is very probably just a local minimum. > -- > -------------------------------------------------------- > Mr. Jussi Lehtola, M. Sc.         Doctoral Student > jussi.lehtola _ helsinki.fi         Department of Physics > http://www.helsinki.fi/~jzlehtol  University of Helsinki > Office phone: +358 9 191 50 632   Finland > -------------------------------------------------------- > Jussi Lehtola, FM                 Tohtorikoulutettava > jussi.lehtola _ helsinki.fi         Fysiikan laitos > http://www.helsinki.fi/~jzlehtol  Helsingin Yliopisto > Työpuhelin: (0)9 191 50 632 > -------------------------------------------------------->      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> > >