From owner-chemistry@ccl.net Fri Sep 18 09:49:01 2015 From: "Abrash, Samuel sabrash\a/richmond.edu" To: CCL Subject: CCL: Inquire a cutoff value for degenerate states Message-Id: <-51751-150918092803-12978-4FCZf+o18et87gL/qlDHkQ],[server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 18 Sep 2015 13:27:56 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash,+,richmond.edu] I don't know the theoretical convention, but from the point of view of a spectroscopist (my original training), .01 eV is 81 cm-1, and while states separated by 81 cm-1 will begin to exhibit Fermi resonance, they would not be considered degenerate. However, the convention for computational chemistry may be based on other arguments. Samuel A. Abrash Associate Professor, Department of Chemistry Coordinator, Environmental Studies Program University of Richmond sabrash]-[richmond.edu Cell: (804) 363-2597 www.richmond.edu/~sabrash "At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came from darkness and they were joined together. Because of this, out of darkness came the light, and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else... the good inclination and the evil inclination, the right and the left." The Zohar -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu]-[ccl.net [mailto:owner-chemistry+sabrash==richmond.edu]-[ccl.net] On Behalf Of Youzhao Lan lyzhao a aliyun.com Sent: Thursday, September 17, 2015 9:01 PM To: Abrash, Samuel Subject: CCL: Inquire a cutoff value for degenerate states Sent to CCL by: "Youzhao Lan" [lyzhao,+,aliyun.com] Dear all, I want to set a small cutoff value for deciding whether two states are degenerate. Is there a generally acceptted value in a.u. or eV unit for this cutoff? e.g., 0.001 a.u. or 0.01 eV? Any help will be appreciated. Lanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Sep 18 12:07:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor!A!fluor.quimica.uniovi.es" To: CCL Subject: CCL: How can I print forces Message-Id: <-51752-150918120427-26719-KBLaIGVubptrV2dFdt7Cxg],[server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 18 Sep 2015 17:46:49 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]=[fluor.quimica.uniovi.es] On Thu, Sep 17, 2015 at 11:40:04AM -0400, samala nagaprasad reddy snpreddy63###gmail.com wrote: > Hello All, > I am calculating numerical frequencies in Molpro. When I check the > outputs (out and log files), its not printing the forces. I hope there > should be some options to print it. I have gone through the manual and > didn't find. I will be thankful to them if some one helps in this regard. Samala, Maybe you could try to be more creative uding google: 'molpro print force constants' gives you something to try. º Good luck, Víctor Luaña -- . . "In science a person can be convinced by a good argument. / `' \ That is almost impossible in politics or religion" /(o)(o)\ (Adapted from Carl Sagan) /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Química Física y Analítica ! the urgent and the important. ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important, ! e-mail: victor++fluor.quimica.uniovi.es ! and the important are never ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. +--------------------------------------------+ (Dwight D. Eisenhower) GroupPage : http://azufre.quimica.uniovi.es/ From owner-chemistry@ccl.net Fri Sep 18 12:45:01 2015 From: "Robert Molt r.molt.chemical.physics{:}gmail.com" To: CCL Subject: CCL: Inquire a cutoff value for degenerate states Message-Id: <-51753-150918104924-11572-fXiAtCTXmcEsuf3eAk9hyw(!)server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 18 Sep 2015 10:49:17 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics/./gmail.com] It's going to be dependent on the system. We need more information from the original question poser about the context. If I said that two electronic states are separated by 0.1 eV, they are roughly degenerate. If you told me the states were separated by 0.01 eV, I would definitely call those electronic states degenerates. But therein lies the issue: relative to the energy scale of electronic states, 0.01 eV is very tiny. By contrast, like Dr. Abrash noted, 0.01 eV is pathetic for certain spectroscopy studies. On 9/18/15 9:27 AM, Abrash, Samuel sabrasha/richmond.edu wrote: > Sent to CCL by: "Abrash, Samuel" [sabrash,+,richmond.edu] > I don't know the theoretical convention, but from the point of view of a spectroscopist (my original training), .01 eV is 81 cm-1, and while states separated by 81 cm-1 will begin to exhibit Fermi resonance, they would not be considered degenerate. However, the convention for computational chemistry may be based on other arguments. > > Samuel A. Abrash > Associate Professor, Department of Chemistry > Coordinator, Environmental Studies Program > University of Richmond > sabrash:richmond.edu > Cell: (804) 363-2597 > www.richmond.edu/~sabrash > "At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came from darkness and they were joined together. Because of this, out of darkness came the light, and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else... the good inclination and the evil inclination, the right and the left." The Zohar > > -----Original Message----- >> From: owner-chemistry+sabrash==richmond.edu:ccl.net [mailto:owner-chemistry+sabrash==richmond.edu:ccl.net] On Behalf Of Youzhao Lan lyzhao a aliyun.com > Sent: Thursday, September 17, 2015 9:01 PM > To: Abrash, Samuel > Subject: CCL: Inquire a cutoff value for degenerate states > > > Sent to CCL by: "Youzhao Lan" [lyzhao,+,aliyun.com] Dear all, > I want to set a small cutoff value for deciding whether two states are degenerate. > Is there a generally acceptted value in a.u. or eV unit for this cutoff? > e.g., 0.001 a.u. or 0.01 eV? > > Any help will be appreciated. > > Lanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > -- Dr. Robert Molt Jr. Visiting Associate Professor of Chemistry Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 From owner-chemistry@ccl.net Fri Sep 18 21:19:01 2015 From: "Michael K Gilson mgilson^_^ucsd.edu" To: CCL Subject: CCL: Blinded prediction challenges for computer-aided drug design and free energy calculations Message-Id: <-51754-150918205204-15925-EjjkVOMaJJhYl8vZB4KiOw[#]server.ccl.net> X-Original-From: "Michael K Gilson" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 18 Sep 2015 17:51:52 -0700 MIME-Version: 1.0 Sent to CCL by: "Michael K Gilson" [mgilson]_[ucsd.edu] Dear Colleagues, We are pleased to announce the first in a series of community-wide, blinded prediction challenges related to computer-aided drug design and organized by the Drug Design Data Resource (D3R; drugdesigndata.org). Grand Challenge 2015: Prediction of ligand poses, and affinity rankings, for the protein targets HSP90 and MAP4K4. Stage 1 predictions are due November 16, 2015; Stage 2 predictions are due February 1, 2016. For details, and to sign up and participate, please see https://drugdesigndata.org/about/grand-challenge-2015 SAMPL5: Prediction of aqueous host-guest binding free energies and, optionally, enthalpies for three host-guest series. A series of aqueous-organic partition coefficients may also be added in the next several weeks. Predictions are due February 1, 2016. For details, and to participate, please see https://drugdesigndata.org/about/sampl5. These challenges are organized by the Drug Design Data Resource, which is based at UC San Diego and supported by a grant (U01GM111528) from the NIH's National Institute of General Medical Sciences. They are made possible by generous donations of data, pre-publication, from AbbVie, Genentech, the CSAR initiative at U. Michigan, and Professors Lyle Isaacs (U. Maryland) and Bruce Gibb (Tulane U.) Best regards, Rommie Amaro, Stephen Burley, Vicki Feher and Michael Gilson Grand Challenge Organizers John Chodera, Michael Gilson, David Mobley, and Michael Shirts SAMPL Organizers