From owner-chemistry@ccl.net Mon Mar 13 03:38:01 2006 From: "Luis Simon luissimonrubio _ hotmail.com" To: CCL Subject: CCL:G: freq calculation on G03 with frozen atoms Message-Id: <-31178-060313033550-9824-b3oQchadfiZQALZReMahJQ:_:server.ccl.net> X-Original-From: "Luis Simon" Date: Mon, 13 Mar 2006 03:35:46 -0500 Sent to CCL by: "Luis Simon" [luissimonrubio+*+hotmail.com] I am trying to find TS structures using G03 in a large molecule, so a initial (and very expensive) hessian is needed. I have observed that the reaction coordinate is only related to a small part of the whole molecule, so I guess that there is no use in calculating the hessian matrix considering all the atoms in the molecule and it will suffice to consider those atoms (and neighbour atoms) that are "active" in the transition state. I have tried to use ONIOM but it fails as some imaginary frequencies are obtained for the low layer. Removing atoms in a freq input files yields a chk file that can not be read in the ts input file. s there any way of simply freezing few atoms in the hessian calculation? I mean, is there some way of indicate to gaussian to skip calculation of some second derivatives and put those derivatives to zero? Thanks in advanced: Luis From owner-chemistry@ccl.net Mon Mar 13 08:55:00 2006 From: "Moreau Yohann yohann.moreau]|[cbt.uhp-nancy.fr" To: CCL Subject: CCL:G: freq calculation on G03 with frozen atoms Message-Id: <-31179-060313084121-12859-VX+Ug78Kc/0J2Pc4wJ345Q++server.ccl.net> X-Original-From: Moreau Yohann Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Mon, 13 Mar 2006 14:10:14 +0200 MIME-Version: 1.0 Sent to CCL by: Moreau Yohann [yohann.moreau]_[cbt.uhp-nancy.fr] Le Lundi 13 Mars 2006 10:58, Luis Simon luissimonrubio _ hotmail.com a écrit : Hi Luis, When computing the normal mode, you can "freeze" some atoms in gaussian, as indicated in an older CCL post : http://www.ccl.net/cgi-bin/ccl/message.cgi?2004+05+27+005 The number of normal modes thus determined will be 3(N-m)*6, for a total number of N atoms with m frozen. However, the hessian matrix will have the dimension of the total system, with zero for elements corresponding to frozen atoms, and the checkpoint file will be usable. Hope this helps, Yohann > Sent to CCL by: "Luis Simon" [luissimonrubio+*+hotmail.com] > I am trying to find TS structures using G03 in a large molecule, so a > initial (and very expensive) hessian is needed. I have observed that the > reaction coordinate is only related to a small part of the whole molecule, > so I guess that there is no use in calculating the hessian matrix > considering all the atoms in the molecule and it will suffice to consider > those atoms (and neighbour atoms) that are "active" in the transition > state. > > I have tried to use ONIOM but it fails as some imaginary frequencies are > obtained for the low layer. Removing atoms in a freq input files yields a > chk file that can not be read in the ts input file. > > s there any way of simply freezing few atoms in the hessian calculation? I > mean, is there some way of indicate to gaussian to skip calculation of some > second derivatives and put those derivatives to zero? > > Thanks in advanced: > > Luis From owner-chemistry@ccl.net Mon Mar 13 09:55:00 2006 From: "Hemant Kumar Srivastava hemantkrsri[*]md.huji.ac.il" To: CCL Subject: CCL:G: Problem in Gaussian-03 calculation Message-Id: <-31180-060313060138-19485-qcQqvXOXLkucMGqhMnWLkw##server.ccl.net> X-Original-From: "Hemant Kumar Srivastava" Date: Mon, 13 Mar 2006 06:01:34 -0500 Sent to CCL by: "Hemant Kumar Srivastava" [hemantkrsri(_)md.huji.ac.il] Dear Researchers, I am working in the Hebrew University of Jerusalem Israel and doing some quantum chemical calculations of some base pairs by using Gaussian-03 package. I have finished the calculation at hf/3-21g and hf/6-31g level, and now I am trying at b3lyp level by reading the geometry from the chk file of hf/6-31g calculation by using the following keyword. ---------------------------------------------------------------------- %chk=eth_g1_test2.chk %mem=25MW %nproc=1 geom=check guess=read opt=modredundant b3lyp nosymm geom=connectivity Title Card Required -1 1 From owner-chemistry@ccl.net Mon Mar 13 12:07:00 2006 From: "Uwe Huniar uwe.huniar * cosmologic.de" To: CCL Subject: CCL: Turbomole 5.8 released Message-Id: <-31181-060313112716-21528-7gF1RwK0KjnGfBLGYDePHQ . server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 13 Mar 2006 16:35:29 +0100 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar,cosmologic.de] Dear colleagues, we are pleased to announce the release of the new Turbomole version 5.8 Turbomole is a very robust and extremely fast quantum chemistry program package developed at the group of Prof. Ahlrichs, University of Karlsruhe. The focus lies in its DFT (ground and excited states, including gradients for TDDFT) and MP2 (ground states) / CC2 (ground and excited states, including gradients) capabilities. With the usage of the RI approximation for DFT and MP2/CC2 it is the program of choice for medium size to large systems, allowing the calculation of systems with several thousand basis functions (example: see below). For a complete list of features and the documentation please visit http://www.turbomole.com Please note that the distribution, maintenance, support, etc. for Turbomole has changed since October, 1st. Please visit http://www.cosmologic.de/info-turbomole.html to get more information about this issue. RELEASE NOTES: TURBOMOLE V5.8 New features include: * Implementation of new basis sets for the elements H - Rn, except lanthanides, which guarantee consistent accuracy across the periodic table. * Small core ECPs for 5p and 6p elements and corresponding basis sets. * ECP routines including g-projectors (energy and gradient only). * Parallel multipole accelerated RI-J (MARI-J). * Faster integral routines, especially for RI treatments. * Improved functionality and simplified handling of tools for molecular properties, wavefunction analysis, and interfaces to visualization tools. * Analytical excited state gradients for RI-CC2. * Parallel RI-MP2 and RI-CC2 ground state and RI-CIS(D), RI-CC2, and RI-ADC(2) excitation energies (ricc2 module). * Full support of the ricc2 program by the input module define. * Additional auxiliary basis sets for RI-MP2/RI-CC2 calculations for the QZVPP (H-Kr) and cc-pwCVXZ (B-Ne, Al-Ar) orbital basis sets. * COSMO with symmetry and more stable A-matrix setup. * Virtual cavities for condensed phases and bond distance constraints added to molecular dynamics. * A new and user-friendly input generator TMOLE with extended functionality (e.g. Z-matrix input, potential curve calculations, generating input and running calculations in one step). * New DIIS methods and damping defaults for accelerated SCF convergence. * Automatic switching from internal coordinates to Cartesians and back in case of internal coordinate failure for minimization and transition state optimization. * Maximum number of atoms and basis functions increased to 700 and 10000 resp. Example for RI-DFT: DFT energy for Crambin, 645 atoms, SV(P) basis with 5578 basis functions, C1 symmetry, on a usual Opteron system with 2.2GHz, serial version only, one SCF iteration takes just half an hour. For a set of (small) benchmarks, initially designed to compare different system architectures, see http://www.turbomole.com -> benchmarks The Turbomole Support Team (Michael Diedenhofen, Uwe Huniar, Andreas Klamt) From owner-chemistry@ccl.net Mon Mar 13 12:41:00 2006 From: "Sergio Emanuel Galembeck segalemb-.-usp.br" To: CCL Subject: CCL:G: Problem in Gaussian-03 calculation Message-Id: <-31182-060313120324-1877-CxYxVehmUy5TIDVFajM8hQ_-_server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Mar 2006 13:02:54 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb~!~usp.br] Dear Hemant, Probably you forgot to indicate the basis set, otherwise G03 will use STO-3G by defaut. Also you put opt=modredundant, but did not indicate the changes in redundant coordinates on the last line of your input file. Best regards, Sergio Galembeck Citando "Hemant Kumar Srivastava hemantkrsri[*]md.huji.ac.il" : > Sent to CCL by: "Hemant Kumar Srivastava" [hemantkrsri(_)md.huji.ac.il] > Dear Researchers, > > I am working in the Hebrew University of Jerusalem Israel and doing some > quantum chemical calculations of some base pairs by using Gaussian-03 > package. I have finished the calculation at hf/3-21g and hf/6-31g level, and > now I am trying at b3lyp level by reading the geometry from the chk file of > hf/6-31g calculation by using the following keyword. > > ---------------------------------------------------------------------- > %chk=eth_g1_test2.chk > %mem=25MW > %nproc=1 > geom=check guess=read opt=modredundant b3lyp nosymm geom=connectivity > > Title Card Required > > -1 1> > > > From owner-chemistry@ccl.net Mon Mar 13 20:26:00 2006 From: "igor novak upper_peirce!A!yahoo.com" To: CCL Subject: CCL: Dalton software Message-Id: <-31183-060313182948-28957-RSfF1FVInX/bKweCTc2DOA{:}server.ccl.net> X-Original-From: "igor novak" Date: Mon, 13 Mar 2006 18:29:47 -0500 Sent to CCL by: "igor novak" [upper_peirce]-[yahoo.com] Dear CCL netters, has anybody compiled Dalton code for AMD64 Athlon CPU?? Regards I.Novak From owner-chemistry@ccl.net Mon Mar 13 21:54:00 2006 From: "Sten Nilsson Lill stenil---chem.gu.se" To: CCL Subject: CCL:G: freq calculation on G03 with frozen atoms Message-Id: <-31184-060313193414-6937-P0TlhzvXJ8sWU5oQQoeXZQ---server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 14 Mar 2006 00:42:17 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil*o*chem.gu.se] Dear Luis, I've found it useful to calculate the second derivative numerically for some variables important for the reaction coordinate. You need to use opt=modredundant and for example if the angle 1-2-3 with a value of 104.5 is important for your reaction coordinate the syntax is to add a D after that variable in your input. See below and also the OPT keyword at gaussian.com 1 2 1.0 2 3 1.5 1 2 3 104.5 D 2 3 4 110.0 Hope it helps! Regards, Sten Nilsson Lill > Sent to CCL by: "Luis Simon" [luissimonrubio+*+hotmail.com] > I am trying to find TS structures using G03 in a large molecule, so a > initial (and very expensive) hessian is needed. I have observed that the > reaction coordinate is only related to a small part of the whole molecule, > so I guess that there is no use in calculating the hessian matrix > considering all the atoms in the molecule and it will suffice to consider > those atoms (and neighbour atoms) that are "active" in the transition > state. > > I have tried to use ONIOM but it fails as some imaginary frequencies are > obtained for the low layer. Removing atoms in a freq input files yields a > chk file that can not be read in the ts input file. > > s there any way of simply freezing few atoms in the hessian calculation? I > mean, is there some way of indicate to gaussian to skip calculation of > some second derivatives and put those derivatives to zero? > > Thanks in advanced: > > Luis> > > > Ph. D. Sten Nilsson Lill Dep. of Chemistry Göteborg University Kemigården 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2901 Fax: +46-31-772 3840 E-mail: stenil###chem.gu.se Alternative e-mail: slill1###lsu.edu From owner-chemistry@ccl.net Mon Mar 13 23:30:00 2006 From: "Sue L chsue2004!A!yahoo.com" To: CCL Subject: CCL: DFT for pi-pi Interaction? Message-Id: <-31185-060313231525-20500-BD4hHRCAZ8uGtGeniPptCA^server.ccl.net> X-Original-From: "Sue L" Date: Mon, 13 Mar 2006 23:15:21 -0500 Sent to CCL by: "Sue L" [chsue2004 .. yahoo.com] Hi, Do you know any DFT method that describes well the pi-pi interaction of the aromatic system? Thank you very much. Sue