From owner-chemistry@ccl.net Fri Jun 15 07:54:01 2007 From: "Marcel Swart marcel.swart .. icrea.es" To: CCL Subject: CCL: Negative frequency problem Message-Id: <-34495-070615075105-6349-DbkfCvGELU+8KEzi7UlWSQ[a]server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Fri, 15 Jun 2007 13:50:40 +0200 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Marcel Swart [marcel.swart _ icrea.es] On Jun 14, 2007, at 10:54 PM, Christopher Cramer cramer,,chem.umn.edu wrote: > There have been several posts recently with questions and > proposed solutions to the problem of "too many negative > frequencies" for transition-state (TS) structures. > > So, what can one do? Some codes permit one to choose a finer > quadrature grid, and this often does solve the problem. Of course, > one can then worry about whether one should go back and recompute > one's full set of stationary points with this finer grid (it's only > computer time...) but at least one knows that the issue is not a > chemical one. Another option is to compute the frequencies by > finite difference of the first derivatives (probably even MORE > expensive and not really an ideal option). Lastly, one can boldly > rely on one's chemical intuition to know when one is being plagued > by this problem and attempt to sleep well while blithely ignoring > the issue (after all, the mode in question will have a "true" > frequency that will contribute negligibly to zero-point vibrational > energy, and negligibly to enthalpy, and will be so small that the > correct value should not be used on the QMHO approximation for > entropy in any case). I would just like to add that ADF has the possibility to scan the normal mode, to verify the corresponding frequencies; with the 2006.01 version, this is being done by default for all imaginary frequencies that are found. This option is related to the (so-called mode-tracking) frequency scanning by Reiher, Neugebauer and co-workers. =================================== dr. Marcel Swart ICREA researcher at Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) fax +34-972-418356 e-mail marcel.swart_-_icrea.es marcel.swart_-_udg.edu web http://www.icrea.es/pag.asp?id=Marcel.Swart http://iqc.udg.edu/~marcel =================================== From owner-chemistry@ccl.net Fri Jun 15 11:31:00 2007 From: "Neil S Ostlund ostlund. ~~ .hyper.com" To: CCL Subject: CCL:G: HyperChem and Gamess, Gaussian, QChem, PQS, and Mopac2007 Message-Id: <-34496-070614123032-8078-QTFxv2D0Qumo+vtFwUoKQQ ~~ server.ccl.net> X-Original-From: "Neil S Ostlund" Date: Thu, 14 Jun 2007 12:30:28 -0400 Sent to CCL by: "Neil S Ostlund" [ostlund]=[hyper.com] The newest Release 8 of HyperChem (www.hyper.com)includes Open Source interfaces that may be of interest to many people on this list. Initially, interfaces are available for PCGamess, WinGamess, PQS, Q-Chem, Gaussian, and Mopac2007 although others can and will be created . The interfaces are works in progress and will be regularly updated with contributions (hopefully) from members of this list as well as others. The interfaces are compilable in Visual Studio C++ and include 3 modes (interactive, batch, and input only). The fully interactive mode uses HyperChem to create a molecule structure, spawn the third-party job, run it, and and parse its output to display densities, orbitals, structures and vibrational modes, etc. The batch mode only spawns the third-party job and then lets it run from HyperChem input. The final mode just creates input files for each of these DOS-like (command line) packages. The interfaces allow one to have a fully graphical user interface to these packages. Initially, only single point, optimization, and vibrational analysis calculations are supported (for SCF calculations) but it is relatively easy to add new dialog boxes, options, etc. For the moment, these HyperChem interfaces are available only for Windows versions of each third-party package (Gamess, etc.) but a client-server (Windows to Linux) version is under way. The interfaces can be downloaded from the above web site. From owner-chemistry@ccl.net Fri Jun 15 12:13:00 2007 From: "Eric Scerri scerri : chem.ucla.edu" To: CCL Subject: CCL: IHPST June Newsletter Message-Id: <-34497-070615115547-19581-yZWazZr5UDUVetKTSbxGIA(~)server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-14--397910074 Date: Fri, 15 Jun 2007 08:10:36 -0700 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Eric Scerri [scerri a chem.ucla.edu] --Apple-Mail-14--397910074 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Begin forwarded message: > From: Michael Matthews > Date: June 14, 2007 11:46:24 PM PDT > To: ihpst-group+*+explode.unsw.edu.au > Subject: IHPST June Newsletter > > Dear IHPST Colleagues, > > The June issue of the IHPST newsletter is now available on the web at: > > http://www.ihpst.org/newsletters.html > > CONTENTS > > 1. 2007 IHPST Conference (Programme) > 2. Science & Education Report (Vol.16 Nos.7-8, Models > special issue) > 3. Notre Dame Summer Program for Secondary Science and > Mathematics Teachers; June 25-29, 2007 > 4. International Society for the Philosophy of Chemistry > (ISPC), 2007 Summer Symposium, August 5-9, San Francisco > 5. Fourth Hellenic Conference on History, Philosophy and > Science Teaching, October 5-7, 2007. > 6. Educators for Sustainability > 7. Current Research > 8. Publications for Sale > 9. Coming Conferences > 10. Future Newsletter Items > 11. IHPST Email List > > In item 1, there are directions for seeing the approximately 160 > presentations being made at the 9th IHPST Conference being held in > Calgary, June 24-28; also information for last-minute registrations. > > > Regards, > > > > Michael R. Matthews > > > > A/Professor Michael R. Matthews > School of Education > University of New South Wales > Sydney, 2052 > Australia > > ph. 61-2-9385.1951 (w) > 61-2-9418.3665 (h) > fax 61-02-9385.1946 > > Secretary, International History, Philosophy & Science Teaching > Group ( www.ihpst.org ) > Editor, 'Science & Education' journal ( www.springer.com/journal/ > 11191) > Coordinator, International Pendulum Project ( www.arts.unsw.edu.au/ > pendulum/ ) > > The Periodic Table: Its Story and Its Significance, by Eric Scerri, Oxford University Press, 2007. ------------------------------------------------------------------------ ----------------------------------------------------------------------- The Periodic Table is one of the most iconic symbols in our culture. Every person interested in the physical world in which we live will want to read this book. It is also a masterful history of the people involved in the establishment of the periodic law of chemistry. The gradual growth in awareness of the regularities of the elements is the main theme of this work. It is already a classic in its first year in print! Gary D. Patterson (Carnegie Mellon University, Pittsburgh, PA) - ------------------------------------------- Dr. Eric Scerri UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Box 951569, Los Angeles, CA 90095-1569. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Periodic Table Website: http://www.allperiodictables.com/apt/ClientPages/Scerripages/Scerri.html Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-14--397910074 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Begin = forwarded message:

From: = Michael Matthews <m.matthews+*+unsw.edu.au>
Date: June 14, 2007 11:46:24 PM = PDT
Subject: IHPST June = Newsletter
= http://www.ihpst.org/newsletters.html
=A0
CONTENTS
=A0
= 1.=A0=A0=A0=A0=A0=A0=A0=A0 2007 IHPST Conference (Programme)
= 2.=A0=A0=A0=A0=A0=A0=A0=A0 Science & Education Report (Vol.16 = Nos.7-8, Models special issue)
3.=A0=A0=A0=A0=A0=A0=A0=A0 Notre Dame = Summer Program for Secondary Science and Mathematics Teachers; June = 25-29, 2007
4.=A0=A0=A0=A0=A0=A0=A0=A0 International Society for the = Philosophy of Chemistry (ISPC), 2007 Summer Symposium, August 5-9, San = Francisco
5.=A0=A0=A0=A0=A0=A0=A0=A0 Fourth Hellenic Conference on = History, Philosophy and Science Teaching, October 5-7, 2007.
= 6.=A0=A0=A0=A0=A0=A0=A0=A0 Educators for Sustainability
7.=A0=A0=A0=A0= =A0=A0=A0=A0 Current Research
8.=A0=A0=A0=A0=A0=A0=A0=A0 = Publications for Sale
9.=A0=A0=A0=A0=A0=A0=A0=A0 Coming = Conferences
10.=A0=A0=A0=A0=A0=A0 Future Newsletter Items
= 11.=A0=A0=A0=A0=A0=A0 IHPST Email List
=A0
In item 1, there are = directions for seeing the approximately 160 presentations being made at = the 9th IHPST Conference being held in Calgary, June 24-28; = also information for last-minute registrations.
=A0
=A0
= Regards,
=A0
=A0
=A0
Michael R. Matthews
=A0
= =A0

A/Professor Michael R. Matthews
School of = Education
University of New South Wales
Sydney, 2052
= Australia

ph. 61-2-9385.1951 (w)
=A0=A0=A0=A0=A0 = 61-2-9418.3665=A0 (h)
fax 61-02-9385.1946

Secretary, = International History, Philosophy & Science Teaching Group ( www.ihpst.org = )
Editor, 'Science & Education'=A0 journal ( = www.springer.com/journal/11191)
Coordinator, International = Pendulum Project ( www.arts.unsw.edu.au/pendulum/ )


=


The Periodic Table: Its Story and = Its Significance, by Eric Scerri, Oxford University Press, = 2007.

The Periodic Table is one of the most iconic symbols = in our culture. Every person interested in the physical world in which = we live will want to read this book. It is also a masterful history of = the people involved in the establishment of the periodic law of = chemistry. The gradual growth in awareness of the regularities of the = elements is the main theme of this work. It is already a classic in its = first year in print!=A0=A0 =A0=A0 =A0Gary D. Patterson (Carnegie Mellon University, = Pittsburgh, PA) = -

Dr. Eric Scerri
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Box = 951569,
Los Angeles,
CA = 90095-1569.

310 206 7443
fax: 310 206 = 2061

UCLA faculty web page:=A0=A0=A0
Periodic Table Website:

Editor of Foundations of Chemistry,

International Society for the Philosophy of = Chemistry,
=
= --Apple-Mail-14--397910074-- From owner-chemistry@ccl.net Fri Jun 15 13:22:00 2007 From: "Kaci Tizi_Ouzou kaci.tiziouzou[-]gmail.com" To: CCL Subject: CCL:G: G03: Gaussian Charge distribution Message-Id: <-34498-070615125819-25568-NQrXYbYpA99BcMtNbUF9Vg^_^server.ccl.net> X-Original-From: "Kaci Tizi_Ouzou" Content-Type: multipart/alternative; boundary="----=_Part_53174_29032485.1181926326109" Date: Fri, 15 Jun 2007 10:52:06 -0600 MIME-Version: 1.0 Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou]=[gmail.com] ------=_Part_53174_29032485.1181926326109 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi folks, Is there a way to set a charge distribution in Gaussian: G03. If I remember well, there used to be a way to define a Gaussian charge density back in Gaussian98 but I could not figure out whether it is possible to do the same in G03. So far, I have seen the keyword "charge" which defines a point charge but I am rather interested in defining a Gaussian density that can represent a charge located at Xc, Yx, Zc Thanks for your help. Cheers Kass ------=_Part_53174_29032485.1181926326109 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi folks,
 
 
Is there a way to set a charge distribution in Gaussian: G03. If I remember well, there used to be a way to define a Gaussian charge density back in Gaussian98 but I could not figure out whether it is possible to do the same in G03.
 
So far, I have seen the keyword "charge" which defines a point charge but I am rather interested in defining a Gaussian density that can represent a charge located at Xc, Yx, Zc
 
 
Thanks for your help.
 
 
Cheers
 
 
Kass
------=_Part_53174_29032485.1181926326109-- From owner-chemistry@ccl.net Fri Jun 15 14:06:00 2007 From: "David A. Case case ~ scripps.edu" To: CCL Subject: CCL: Problems about AMBER Message-Id: <-34499-070613170007-2622-8MtSGoS+eigd+zJ5jcvGYQ_-_server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 13 Jun 2007 13:59:44 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case(_)scripps.edu] On Wed, Jun 13, 2007, littlecan p9894105%x%mail.ncku.edu.tw wrote: > > Recently, I started using AMBER and have encountered problems regarding van > der waals energy calculation. It is far better to submit Amber-related questions to the Amber mailing list; see http://amber.scripps.edu for information on how to subscribe and post. > We are not sure about either our calculation is incorrect or it is > reasonable to have positive van der waals energy in those cases. There is nothing intrinsically suprising about have a postive value here. > > 2. In the 1995 paper by Cornell et al., the scale factor of > 1/2.0 is recommended for reducing the 1-4 VDW interactions as used > previously by Weiner et al. (lines 6 to 8 from the bottom of the right-hand > column in page 5183). Is our interpretation correct? This sounds correct to me. ...regards...dave case From owner-chemistry@ccl.net Fri Jun 15 15:36:00 2007 From: "rasesh78^^WPI.EDU" To: CCL Subject: CCL: diffusion in zeolite Message-Id: <-34500-070614234737-21435-w80mXWY/VQeImcK62Mp+wQ a server.ccl.net> X-Original-From: rasesh78:WPI.EDU Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 14 Jun 2007 22:48:14 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: rasesh78^^^WPI.EDU It would be interesting to look at Towhee , especially the electrostatic interactions are important to you ...Here is the link..... http://towhee.sourceforge.net/ Thanks, Rasesh > Bonjour, > > We are looking for a FREE program in MM or QM/MM to study: > - the diffusion of organic molecules in zeolites (FAU X or Y: Si, O, Al, > Na or Cs, H) > - the desorption of organic molecules from zeolite to water or organic > solvant such as n-heptane (interface solid/liquid). > > Music http://zeolites.cqe.northwestern.edu/Music seems appropriate. > > What else ? References ? > > Bonne journée > > Gilles Frapper > groupe chimie quantique appliquée > UMR CNRS 6503 - LACCO - Université de Poitiers > 40, av. recteur Pineau 86022 Poitiers cedex > tel : 05 49 45 35 74 - mel : gilles.frapper(~)univ-poitiers.fr > site : http://labo.univ-poitiers.fr/yargla > > From owner-chemistry@ccl.net Fri Jun 15 16:11:00 2007 From: "rasesh78-,-WPI.EDU" To: CCL Subject: CCL: diffusion in zeolite Message-Id: <-34501-070614234729-21387-MKOnjLcvikrgO1t75/TkYQ---server.ccl.net> X-Original-From: rasesh78*WPI.EDU Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 14 Jun 2007 22:49:34 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: rasesh78:+:WPI.EDU Also DLPOly is a good one for MD simulations in Zeolites.... > Bonjour, > > We are looking for a FREE program in MM or QM/MM to study: > - the diffusion of organic molecules in zeolites (FAU X or Y: Si, O, Al, > Na or Cs, H) > - the desorption of organic molecules from zeolite to water or organic > solvant such as n-heptane (interface solid/liquid). > > Music http://zeolites.cqe.northwestern.edu/Music seems appropriate. > > What else ? References ? > > Bonne journée > > Gilles Frapper > groupe chimie quantique appliquée > UMR CNRS 6503 - LACCO - Université de Poitiers > 40, av. recteur Pineau 86022 Poitiers cedex > tel : 05 49 45 35 74 - mel : gilles.frapper(~)univ-poitiers.fr > site : http://labo.univ-poitiers.fr/yargla > >