From owner-chemistry@ccl.net Wed Sep 26 04:52:01 2007 From: "Lukasz Cwiklik lukasz.cwiklik{=}uochb.cas.cz" To: CCL Subject: CCL: display charge density and local potential of VASP calculations Message-Id: <-35253-070925205700-31048-T5kqwylpXFWd1vtNbbRIvg(-)server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 25 Sep 2007 16:18:40 -0700 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [lukasz.cwiklik|a|uochb.cas.cz] On 9/25/07, jim li g_p_li__yahoo.com wrote: > > > > Hello: > > I use VASP to do the calculations. > I am looking for a graphics program to display VASP charge density, local > potential, geometric structure, band structure, density of states, geometry > and electron density, and local potential and geometry together. > Any help is appreciated. Hello Jim, Maybe you should look at VASP Plugin for VMD: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/vaspplugin.html Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Wed Sep 26 05:41:00 2007 From: "Herbert Fruchtl herbert.fruchtl~~st-andrews.ac.uk" To: CCL Subject: CCL:G: Relaxed PES in g03 using forcefield? Message-Id: <-35254-070926053618-7032-K6On1L9veuAbMNKbMh3bNw!A!server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 Sep 2007 10:35:41 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl ~~ st-andrews.ac.uk] You need to use the optimization algorithm for "small" molecules (which is not the default for MM and semiempirical methods) to use ModRedundant: Opt=(Small,ModRedundant) HTH, Herbert Ben King king:-:chem.unr.edu wrote: > > Sent to CCL by: Ben King [king^chem.unr.edu] > Dear CCLers: > > Summary: how can one use gaussian to perform a relaxed potential energy > scan with a force field? > > We need to generate a 2-D potential energy surface for a bond-breaking > coupled with a torsion. Gaussian's tools for performing a relaxed PES > using the modredundant option to opt are ideal, but Z-matrix tools could > also work. Here is the problem: Gaussian (g03) completely ignores any > constraints when we use molecular mechanics (amber, uff, etc.), using > either Z-matrices or opt=modredundant. This also happens in OMION > methods using a MM fragment. Our syntax is correct, as we do these same > calculations (albeit inaccurately and only over limited portions of the > PES) using semi-empirical methods. > > We must use a molecular mechanics force field: van der Waals interaction > are important in our molecule and we need to study the portion of the > bond dissociation region that is poorly described by single references > wavefunctions (e.g., C-C bond distances of 1.4 A to 6.0 A in 0.2 A > increments). The molecule is large (C62H38), so high-level ab initio > methods are prohibitively time consuming. Molecular mechanics will give > us the most realistic description of the molecular behavior, provided > that we use a Morse potential for the bond dissociation. > > If anyone can suggest a procedure to generate a PES from a force field, > I would be grateful. This is one of those irritating things that should > be easy but ends up being exceptionally difficult. Also, if anyone > knows why Gaussian behaves so oddly with MM methods, I would be > delighted to know. > > Thanks, > > Ben > > p.s. The version of Gaussian is: Gaussian 03: AM64L-G03RevC.02 > 12-Jun-2004 > p.p.s. We are limping through this by running thousands of individual > constrained optimizations using Tinker, but it isn't pretty... > > ---- > Benjamin T. King, Associate Professor > Department of Chemistry/216 > University of Nevada, Reno 89557 > tel (775) 784-1736 fax (775) 784-6804 > king^_^chem.unr.edu > http://www.chem.unr.edu/faculty/btk/http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Wed Sep 26 08:45:00 2007 From: "Tom de Greef t.f.a.d.greef++tue.nl" To: CCL Subject: CCL:G: Visualising electric transition dipole moments from TDDFT calculations Message-Id: <-35255-070926035603-4929-BtWA30TPkRyyKhhiK5KjLw]-[server.ccl.net> X-Original-From: "Tom de Greef" Date: Wed, 26 Sep 2007 03:55:59 -0400 Sent to CCL by: "Tom de Greef" [t.f.a.d.greef * tue.nl] Dear all, Thanks a lot with the previous respons on my question regarding visualising the PCM cavity. However, I now have a new (noob) question. I want to visualise the electric transition dipole moments from TDDFT calculation from Gaussian. Does anyone know a free (Linux, Windows) program that can do the trick? Wishing you all the best, Tom From owner-chemistry@ccl.net Wed Sep 26 09:20:00 2007 From: "Md. Ehesan Ali ehesan+*+gmail.com" To: CCL Subject: CCL: display charge density and local potential of VASP calculations Message-Id: <-35256-070925212143-10972-lf9JTXZ1wkgJpwvfis/z6Q()server.ccl.net> X-Original-From: "Md. Ehesan Ali" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 26 Sep 2007 01:39:14 +0200 MIME-Version: 1.0 Sent to CCL by: "Md. Ehesan Ali" [ehesan*gmail.com] 'p4vasp' can help you. http://cms.mpi.univie.ac.at/odubay/p4vasp/intro/intro.html regards, Ehesan On 9/25/07, jim li g_p_li__yahoo.com wrote: > > > > Hello: > > I use VASP to do the calculations. > I am looking for a graphics program to display VASP charge density, local > potential, geometric structure, band structure, density of states, geomet= ry > and electron density, and local potential and geometry together. > Any help is appreciated. > > Jim > > ________________________________ > Moody friends. Drama queens. Your life? Nope! - their life, your story. > Play Sims Stories at Yahoo! Games. > > --=20 Md. Ehesan Ali Theoretical Magnetism Group Depart of Physics, University of Uppsala =C5ngstr=F6mlaboratoriet, Box 530, 751 21 UPPSALA, Sweden Ph. No. (+46) 018-471 37 44 (office) (+46) 0735758544 (Mobile) Website: http://ehesan.googlepages.com From owner-chemistry@ccl.net Wed Sep 26 10:20:01 2007 From: "Steve Bowlus chezbowlus : comcast.net" To: CCL Subject: CCL: EPR/ESR simulations Message-Id: <-35257-070926100426-32726-5BIUjp1dmCLo1GhO2w6HDA|a|server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 Sep 2007 06:28:04 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus]^[comcast.net] This is new for me - Can someone point me to a program that will calculate and display a simulated EPR Spectrum? We can already calculate the g-tensor, A-tensor, and Q-tensor. What else might be needed? We are particularly interested in EPR of iron-containing compounds. Cheers, Steve Bowlus From owner-chemistry@ccl.net Wed Sep 26 19:34:01 2007 From: "Close, David M. CLOSED]=[mail.etsu.edu" To: CCL Subject: CCL: EPR/ESR simulations Message-Id: <-35258-070926193046-13768-CB9+/DfIXsd2Xp7TIVFGDw]*[server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Wed, 26 Sep 2007 19:30:33 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED[#]mail.etsu.edu] Steve: Bruker EPR supplies users of their equipment with a CD that has a suite of programs called SimFonia. This will work for your application. There are other solutions in the literature. The old FORTRAN program by Maurani has recently been updated to treat quadrupole interactions. The problems is with metals one has very large hyperfine couplings, and some programs will only treat cases where the hyperfine couplings are small compared to the electron Zeeman term. If your hyperfine couplings are very large, then you must use a treatment developed by John Weil. I have a FORTRAN copy of the revised Maurani program if you can compile a FORTRAN program. Regards, Dave Close. -----Original Message----- > From: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net]=20 Sent: Wednesday, September 26, 2007 9:28 AM To: Close, David M. Subject: CCL: EPR/ESR simulations Sent to CCL by: Steve Bowlus [chezbowlus]^[comcast.net] This is new for me - Can someone point me to a program that will calculate and display a simulated=20 EPR Spectrum? We can already calculate the g-tensor, A-tensor, and Q-tensor.=20 What else might be needed? We are particularly interested in EPR of=20 iron-containing compounds. Cheers, Steve Bowlus -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Sep 26 23:44:01 2007 From: "Anatoli Korkin a_korkin^_^yahoo.com" To: CCL Subject: CCL: Nanotechnology, IoP Publishing: special issue on molecular an bioelect Message-Id: <-35259-070926234239-19650-LT+Jd5m5kGSRrjTm0A0feg_-_server.ccl.net> X-Original-From: "Anatoli Korkin" Date: Wed, 26 Sep 2007 23:42:35 -0400 Sent to CCL by: "Anatoli Korkin" [a_korkin(0)yahoo.com] Further rapid progress of electronics, in particular the increase of computer power and breakthroughs in sensor technology for industrial, medical diagnostics and environmental applications, strongly depends on the scaling of electronic devices, ultimately to the size of molecules. Design of controllable molecular-scale devices may resolve the problem of energy dissipation at the nanoscale and take advantage of molecular self-assembly in the so-called bottom-up approach. The team from the journal Nanotechnology (IOP Publishing, UK (1)) in collaboration with NGC2007 (2) organizers (guest editors: P. Krstic, E. Forzani, NJ Tao and A. Korkin) have published a special issue of the journal on molecular and biolectronics (3). Papers contained in this special issue are selected from the symposium Nano and Giga Challenges in Electronics and Photonics: From Atoms to Materials to Devices to System Architecture (1216 March, 2007, Phoenix, Arizona, USA), as well as from original and novel scientific contributions of invited world-renown researchers. It addresses both theoretical and experimental achievements in the fields of molecular and bioelectronics, chemical and biosensors at the molecular level, including carbon nanotubes, novel nanostructures, as well as related research areas and industrial applications. This special issue of Nanotechnology is devoted to a better understanding of the function and design of molecular-scale devices that are relevant to future electronics and sensor technology. Papers contained in this special issue are selected from the symposium Nano and Giga Challenges in Electronics and Photonics: From Atoms to Materials to Devices to System Architecture (1216 March, 2007, Phoenix, Arizona, USA), as well as from original and novel scientific contributions of invited world-renown researchers. It addresses both theoretical and experimental achievements in the fields of molecular and bioelectronics, chemical and biosensors at the molecular level, including carbon nanotubes, novel nanostructures, as well as related research areas and industrial applications. The conference series Nano and Giga Challenges in Electronics and Photonics was launched as a truly interdisciplinary forum to bridge scientists and engineers to work across boundaries in the design of future information technologies, from atoms to materials to devices to system architecture. Following the first two successful meetings in Moscow, Russia (NGCM2002) and Krakow, Poland (NGCM2004), the third Nano and Giga Forum (NGC2007) was held in 2007 hosted by Arizona State University. The NGC2007 meeting (1), which included two days of tutorials (Spring School) and a three day symposium, attracted approximately 400 participants from academic, industrial and governmental research institutions from 41 countries, and covered recent developments in the fabrication and functionality of nano-scale materials, devices and system architecture from advanced CMOS to molecular electronics, photonics, optoelectronics and magnetic materials and devices. The success of the conference would not have been possible without generous support from many sponsors, governmental, academic and industrial organizations: universities, companies, funding agencies and professional media centers (4) (1) http://www.iop.org/journals/nano (2) http://asdn.net/ngc2007/ (3) http://www.iop.org/EJ/toc/0957-4484/18/42 (4) http://asdn.net/ngc2007/our_sponsors.shtml