From owner-chemistry@ccl.net Wed Oct 18 04:34:01 2006 From: "Pierre Archirel pierre.archirel . lcp.u-psud.fr" To: CCL Subject: CCL:G: answer about SDD basis and pseudo Message-Id: <-32827-061017101112-24063-B8EGDqOhk687y6+JjOy1sg|*|server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 17 Oct 2006 15:18:43 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel-*-lcp.u-psud.fr] This is an answer to M. Tassell: If you use gaussian, SDD basis and pseudos are internaly coded. This is my input for a platinum complex. Note that SDD bases have no polarisation functions, I use extrabasis for this purpose. # b3lyp sddall extrabasis opt Pt(II) (NH3)2 Cl2 0 1 Pt 9.000000 0.000000 -10.550000 Cl 9.000000 0.000000 -8.270000 Cl 9.000000 0.000000 -12.830000 N 7.010000 0.000000 -10.550000 H 6.676667 0.816497 -11.021405 H 6.676667 -0.816497 -11.021405 H 6.676667 -0.000000 -9.607191 N 10.990000 0.000000 -10.550000 H 11.323333 0.816497 -10.078596 H 11.323333 -0.816497 -10.078596 H 11.323333 -0.000000 -11.492809 N 0 d 1 0.8 **** Cl 0 d 1 0.75 **** __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel|*|lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Wed Oct 18 08:57:01 2006 From: "Alon Eisenstein aloneis#%#bgu.ac.il" To: CCL Subject: CCL:G: Gaussian Spin density calculation Message-Id: <-32828-061018050333-9493-EGRTAdgDF4nfe7jSTPhgpQ\a/server.ccl.net> X-Original-From: "Alon Eisenstein" Date: Wed, 18 Oct 2006 05:03:32 -0400 Sent to CCL by: "Alon Eisenstein" [aloneis*bgu.ac.il] Hello, I would like to perform a spin density calculation. I found this when I looked it up in google: http://scgc.epfl.ch/load/cours_chim/ESR/Gaussian.html And I would like to know which basis set to use and how to specify one if an external basis set is required. Thank you, Alon From owner-chemistry@ccl.net Wed Oct 18 18:43:01 2006 From: "Eric Hu list.eric],[gmail.com" To: CCL Subject: CCL: rigid body MD Message-Id: <-32829-061017212220-11408-tMzFEfjrpd8pX5/cyyFrpg!^!server.ccl.net> X-Original-From: "Eric Hu" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 17 Oct 2006 17:19:31 -0700 MIME-Version: 1.0 Sent to CCL by: "Eric Hu" [list.eric###gmail.com] Hello, I'm looking for a molecular dynamics package that is able to rigidify some portion of the system during simulation. So far I have to use an all-atom force field such as Amber. I heard that there was a program called MBO(N)D developed by Moldyn. It disappeared long time ago since the company was bought and its parent company is later gone too. Can anyone point out any available similar programs? Thanks. -Eric From owner-chemistry@ccl.net Wed Oct 18 19:37:00 2006 From: "Venable, Richard \(NIH/NHLBI\) E venabler/a\nhlbi.nih.gov" To: CCL Subject: CCL: rigid body MD Message-Id: <-32830-061018050333-12345-0Etum3y5MAX41u1rXSmW1A]=[server.ccl.net> X-Original-From: "Venable, Richard \(NIH/NHLBI\) [E]" Date: Wed, 18 Oct 2006 19:22:15 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard \(NIH/NHLBI\) [E]" [venabler-.-nhlbi.nih.gov] I'm not sure how well it works, but the MBO(N)D code has been a part of the CHARMM package for quite a while. -- Rick Venable 29/500 Membrane Biophysics Section NIH/NHLBI Lab. of Comp. Biology Bethesda, MD 20892-8014 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov -----Original Message----- From: Eric Hu list.eric],[gmail.com [mailto:owner-chemistry*ccl.net] Sent: Wed 18-Oct-06 6:45 PM To: Venable, Rick Subject: CCL: rigid body MD Sent to CCL by: "Eric Hu" [list.eric###gmail.com] Hello, I'm looking for a molecular dynamics package that is able to rigidify some portion of the system during simulation. So far I have to use an all-atom force field such as Amber. I heard that there was a program called MBO(N)D developed by Moldyn. It disappeared long time ago since the company was bought and its parent company is later gone too. Can anyone point out any available similar programs? Thanks. -Eric From owner-chemistry@ccl.net Wed Oct 18 20:22:00 2006 From: "Jeff Hammond jhammond_+_uchicago.edu" To: CCL Subject: CCL: Effect of basis set on frequency calculations with g03 Message-Id: <-32831-061018133743-26587-oVS5ofrK3YuyycctTn+j7A]|[server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Oct 2006 11:47:26 -0500 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jhammond]-[uchicago.edu] 3-21G is a toy basis set. If the results of a 3-21G calculation were closer to experiment than a 6-311+G(d) calculation, the most you could possibly conclude is that your level of theory, in this case, B3LYP, was insufficient, and you should probably just conclude nothing and run more calculations. B3LYP isn't a rigorously defined method, but it is variational. Bigger basis sets ~should~ always be better. Recently, there has been a debate in CPL over the validity of the immediately preceding statement. See the following two articles and comments thereto if you're interested. R.A. Klein, M.A. Zottola, Chem. Phys. Lett. 419 (2006) 254. R.A. Klein, M.A. Zottola, Chem. Phys. Lett. 421 (2006) 595. You can try MP2, other functionals, and perhaps MRPT2 or CCSD, and more basis sets to get a better handle on what theory best describes your system. If you ran a Dunning series, it would indicate the rate of convergence with respect to zeta-level more definitively than the Pople family, for which triple-zeta isn't really triple-zeta quality according to Schaefer and co-workers in JCP, if my memory serves me right. Jeff From owner-chemistry@ccl.net Wed Oct 18 21:33:01 2006 From: "John Daily john.daily-*-colorado.edu" To: CCL Subject: CCL: rigid body MD Message-Id: <-32832-061018204746-9077-JuTdBQlAwEamcQk8duHl8A~!~server.ccl.net> X-Original-From: John Daily Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 18 Oct 2006 18:34:07 -0600 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: John Daily [john.daily%x%colorado.edu] Eric, I would suggest the Tinker program family. It will allow you to specify that certain portions of a structure be held rigidly. John On Oct 18, 2006, at 4:56 PM, Eric Hu list.eric],[gmail.com wrote: > Sent to CCL by: "Eric Hu" [list.eric###gmail.com] > > Hello, > I'm looking for a molecular dynamics package that is able to rigidify > some portion of the system during simulation. So far I have to use an > all-atom force field such as Amber. I heard that there was a program > called MBO(N)D developed by Moldyn. It disappeared long time ago since > the company was bought and its parent company is later gone too. Can > anyone point out any available similar programs? Thanks. > > -Eric > > > > -= 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/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > >