From owner-chemistry@ccl.net Fri Sep 26 05:38:01 2008 From: "Pierre Archirel pierre.archirel[a]lcp.u-psud.fr" To: CCL Subject: CCL:G: answer to : PCM vs Onsager Message-Id: <-37807-080925121201-30953-I1BwW//APsEA+pTKJb6dog\a/server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 25 Sep 2008 16:17:58 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel*|*lcp.u-psud.fr] Dear colleague, I have no opinion about your specific system, I here only comment on cavity shapes in the PCM method. By Onsager you refer to a spherical cavity, I guess. My experience is: 1- global spherical cavities and local polyatomic ones (for CH3, NH... like in UAKS) can be useful for energies but should not be used for geometry optimisations. 2- at least the "escaped charge" should be controled, i.e. the electron population lying outside the cavity (i.e. inside the dielectric, where all electrostatic interactions are divided by eps, dielectric constant). In G03 it is given by "error on total polarization charges" I consider the value .05 acceptable, larger values worrying. 3- I have observed that geometry optimisation inside a sphere sometimes produces spurious CH dissociations. In other cases I got oscillations between two solutions, with electrons getting in and out of the dielectric (it was an anion). In conclusion geometries should be optimised only with sophisticated cavities, with spheres on every atom, including H, and the escaped charge carefully checked, especially for anions. Pierre Archirel LCP, Universite d'Orsay, France pierre.archirel_+_lcp.u-psud.fr __________________________________________________________ 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 Fri Sep 26 07:00:00 2008 From: "Vincenzo Verdolino vincenzo.verdolino{=}nemo.unipr.it" To: CCL Subject: CCL:G: answer to : PCM vs Onsager Message-Id: <-37808-080926065721-553-wi47wHlGVshWe6S2xH7wtg++server.ccl.net> X-Original-From: "Vincenzo Verdolino" Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 26 Sep 2008 12:56:59 +0200 MIME-Version: 1.0 Sent to CCL by: "Vincenzo Verdolino" [vincenzo.verdolino() nemo.unipr.it] Dear colleague, I'm agree with Pierre Archirel, and I just whant to point out that you have to be careful with the choice of the cavity model. In particular you have to remember that both the UAKS and the corresponding UAHF are fitted respectively for DFT and HF levels. So I suggest to use UA0 or the UFF which explicit all the hydrogen cavities. By the way of charges excape, there are two principal ways I use to fix the problem: 1)using the key icomp, but this way is now obsolete 2)using the iefpcm rather than pcm or cpcm. Has been demonstrated that the integral formalism bypass the problem Vincenzo On Thu, 25 Sep 2008 16:17:58 +0200, Pierre Archirel pierre.archirel[a]lcp.u- psud.fr wrote > Sent to CCL by: Pierre Archirel [pierre.archirel*|*lcp.u-psud.fr] > > Dear colleague, > I have no opinion about your specific system, I here only comment on > cavity shapes > in the PCM method. By Onsager you refer to a spherical cavity, I guess. > My experience is: > 1- global spherical cavities and local polyatomic ones (for CH3, > NH... like in UAKS) can be useful for energies but should not be > used for geometry optimisations. 2- at least the "escaped charge" > should be controled, i.e. the electron population lying outside the > cavity (i.e. inside the dielectric, where all electrostatic interactions > are divided by eps, dielectric constant). In G03 it is given by > "error on total polarization charges" > I consider the value .05 acceptable, larger values worrying. > 3- I have observed that geometry optimisation inside a sphere > sometimes produces spurious CH dissociations. In other cases I got > oscillations between two solutions, with electrons getting in and > out of the dielectric (it was an anion). > > In conclusion geometries should be optimised only with sophisticated > cavities, > with spheres on every atom, including H, and the escaped charge > carefully checked, > especially for anions. > > Pierre Archirel > LCP, Universite d'Orsay, France > pierre.archirel*lcp.u-psud.fr > > __________________________________________________________ > > 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 > __________________________________________________________ > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the % sign. You can > also> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)-- Universita' degli Studi di Parma (http://www.unipr.it) From owner-chemistry@ccl.net Fri Sep 26 18:32:01 2008 From: "Oscar Odio odio__imre.oc.uh.cu" To: CCL Subject: CCL: Connolly Surfaces Message-Id: <-37809-080926115523-22800-WAblihHHRp0J61iRYD+s6w]*[server.ccl.net> X-Original-From: "Oscar Odio" Date: Fri, 26 Sep 2008 11:55:18 -0400 Sent to CCL by: "Oscar Odio" [odio~!~imre.oc.uh.cu] Hello, CCLers: Could you tell me what softwares (better if they are free) can calculate Connolly surfaces? Thanks in advance From owner-chemistry@ccl.net Fri Sep 26 20:24:00 2008 From: "Elaine Meng meng,cgl.ucsf.edu" To: CCL Subject: CCL: Connolly surfaces Message-Id: <-37810-080926192732-4058-zZlk6rggq8dixYUQZRMiQg(_)server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 26 Sep 2008 19:27:28 -0400 Sent to CCL by: "Elaine Meng" [meng*o*cgl.ucsf.edu] Hi Oscar, Many programs calculate Connolly surfaces, but to name just a couple, you may want to take a look at: UCSF Chimera (currently uses Sanner's MSMS for surface calculation) - free download for noncommercial use http://www.cgl.ucsf.edu/chimera/index.html DMS - open source, also downloadable from the UCSF Computer Graphics Lab http://www.cgl.ucsf.edu/Overview/software.html#dms http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html If you are referring not only to the surfaces but to the output file format, both Chimera and DMS can write out dot surfaces of that type. Best, Elaine ----- Elaine C. Meng, Ph.D. meng-.-cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html P.S. this page by Mike Connolly may be of interest: http://www.netsci.org/Science/Compchem/feature14e.html