From owner-chemistry@ccl.net Fri Jan 22 05:45:01 2010 From: "R Chowdhury crajib2009+*+yahoo.com" To: CCL Subject: CCL:G: Eigenvectors in Gaussian 09w Message-Id: <-41096-100122053845-28667-jW4mtityKirPmvh88S6b9A:+:server.ccl.net> X-Original-From: "R Chowdhury" Date: Fri, 22 Jan 2010 05:38:37 -0500 Sent to CCL by: "R Chowdhury" [crajib2009\a/yahoo.com] Dear CCL experts, I would like to extract the eigenvectors of any system from Gaussian 09 after frequency analysis. Please could anybody give some hints on this. Regards, Rajib From owner-chemistry@ccl.net Fri Jan 22 08:48:01 2010 From: "Md Mehboob Alam mehboob.cu~~gmail.com" To: CCL Subject: CCL: Abnormal termination of DALTON job Message-Id: <-41097-100121052226-10247-sd3I4UxXtGTQDBdiwicT9w++server.ccl.net> X-Original-From: "Md Mehboob Alam" Date: Thu, 21 Jan 2010 05:22:22 -0500 Sent to CCL by: "Md Mehboob Alam" [mehboob.cu===gmail.com] Dear all, I am trying to run a job in DALTON for a quadratic response but the job is terminated at a specific point showing the error --- SEVERE ERROR, PROGRAM WILL BE ABORTED --- ERROR (GPOPEN) UPON OPENING A FILE can you please tell me what is the error? Thank you From owner-chemistry@ccl.net Fri Jan 22 10:14:01 2010 From: "Markus Dittrich dittrich:_:psc.edu" To: CCL Subject: CCL: Workshop on Computational Biophysics using NAMD and VMD Message-Id: <-41098-100122094720-13463-3RpsV2yi+fftzOctASjPbg*o*server.ccl.net> X-Original-From: "Markus Dittrich" Date: Fri, 22 Jan 2010 09:47:17 -0500 Sent to CCL by: "Markus Dittrich" [dittrich**psc.edu] Dear Colleagues, The National Resource for Biomedical Supercomputing () at the Pittsburgh Supercomputing Center () and Carnegie Mellon University (www.cmu.edu) will host a 'Hands-On' Workshop on Computational Biophysics using NAMD and VMD. The workshop will be held May 10-14, 2010 at the Pittsburgh Supercomputing Center in Pittsburgh, Pennsylvania. The workshop will be presented by members of the Theoretical and Computational Biophysics Group () at the University of Illinois at Urbana-Champaign and will explore a wide range of physical models and computational approaches for the simulation of biological systems. Workshop material will be based on case studies including the properties of membranes and membrane proteins, the mechanism of molecular motors, and trafficking in the living cell through water and ion channels, as well as signaling pathways. Required physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, and steered molecular dynamics simulations. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills and expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions (mornings) will be accompanied by hands-on computer labs (afternoons) in which students will be able to set up and run simulations. Applications are due by March 15, 2010 and selected participants will be notified by March 22, 2010. Registration will be free of charge for attendees from non-profit academic institutions, and, in addition, the National Resource for Biomedical Supercomputing will cover housing costs. Participants are, however, required to cover their own travel expenses. Due to space constraints, the workshop will be limited to 25 participants. To apply online, please visit: We look forward to receiving your application. For more information, please contact NRBSC Administrator Christal Banks at cbanks.at.psc.edu. From owner-chemistry@ccl.net Fri Jan 22 15:11:00 2010 From: "Jim Kress ccl_nospam===kressworks.com" To: CCL Subject: CCL: Atomic Density Problem Message-Id: <-41099-100121195851-21266-QUYTrSrp9L7mZchAfJ2zPg,server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 21 Jan 2010 16:48:03 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam ~ kressworks.com] Did you try ChemCraft, gOpenMol, Facio, Molekel, Discovery Studio or Mercury? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com=-=ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com=-=ccl.net] On Behalf Of Brian Salter-Duke > Brian.James.Duke..gmail.com > Sent: Monday, January 18, 2010 3:30 PM > To: Kress, Jim > Subject: CCL: Atomic Density Problem > > > Sent to CCL by: Brian Salter-Duke [Brian.James.Duke^-^gmail.com] > On Mon, Jan 18, 2010 at 01:23:11PM +0100, Prasenjit SEAL > prasenjit.seal#crm2.uhp-nancy.fr wrote: > > > > Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr] > > Hello, > > > > Thanks for the reply... > > > > However, that is not what I meant. I mean to say that suppose I have a > > cube file of 'water' molecule containing the charge densities at each > > grid point. Obviously, one has to specify the number of grid points > > along with the grid spacing. Now I want to calculate the free atomic > > densities (which has to be spherical in nature irrespective of the atom) > > of the two H atoms and one O atom present in H2O using that molecular > > cube file. > > How do you define the free atomic densities? These are for the "free" > atoms and therefore have nothing to do with the results you have for the > density of the water molecule, so you can not use that molecular cube > file. You may have to do separate calculations for each atom. What do > you want them for? > > Brian. > > > If any Fortran code is available which can read the molecular cube file > > of a system and can calculate the spherically averaged free atomic > > densities for the constituent atoms, then it would be very helpful. > > > > Cheers, > > > > Prasenjithttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > -- > Brian Salter-Duke (Brian Duke) > 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. > Email: b_duke/./bigbond.net.au Phone: 03-93992847 > Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm From owner-chemistry@ccl.net Fri Jan 22 16:45:00 2010 From: "Tim Holme tholme**stanford.edu" To: CCL Subject: CCL:G: gaussian polarizability: units and interpretations. Message-Id: <-41100-100122140653-17345-dQzLCgldDzoBooaMiet3ug ~~ server.ccl.net> X-Original-From: "Tim Holme" Date: Fri, 22 Jan 2010 14:06:49 -0500 Sent to CCL by: "Tim Holme" [tholme()stanford.edu] I have two questions about calculating polarizability in Gaussian with the polar keyword: 1. The output contains an isotropic polarizability, then the lower diagonal portion of a matrix, then a hyperpolarizability. Is that lower diagonal matrix also in units of volume? It is to be added to the isotropic polarizability? Next, is the hyperpolarizability in units of dipole/field , i.e. C m^2/V? 2. What is the difference between a freq,polar calculation and a polar calculation? It looks like freq,polar will calculate a dielectric constant for a given frequency of applied electric field, is this correct? Thanks for your help, Tim