From owner-chemistry@ccl.net Sat Jan 28 00:15:01 2006 From: "Marcel Swart m.swart]|[few.vu.nl" To: CCL Subject: CCL:G: composite energy method with transition metal Message-Id: <-30670-060127160010-27934-YpJe0mX3XftZffj4CekFZg/./server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-19--974390893 Date: Fri, 27 Jan 2006 21:34:42 +0100 Mime-Version: 1.0 (Apple Message framework v553) Sent to CCL by: Marcel Swart [m.swart() few.vu.nl] --Apple-Mail-19--974390893 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed On Friday, January 27, 2006, at 01:00 AM, Young Leh=20 youngleh-#-gmail.com wrote: > I have been collecting information on the application of composite=20 > energy methods to transition metals for a long time. All the popular=20= > composite energy methods, Gaussian-n, Complete Basis Set, and=20 > multi-coefficent, are only calibarited with first, second, and third=20= > row elements excluding transition metals. Is there any composite=20 > energy method that can be applied to transition metal at all? Or if I=20= > am going to use those methods to transition metals, how wrong could I=20= > be? Probably very wrong, because the transition metals are in a league of=20 their own; see for instance the following paper for a systematic study on the=20 performance of DFT functionals for spin state energies (note: spin state energies are=20= even more difficult than "regular" energies): J. Phys. Chem. A 2004 ,108 , 5479-5483 M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma "Validation of exchange-correlation functionals for spin states of=20 iron-complexes" Note also that for instance for ferrocene, the Fe-ring distance is overestimated by RHF by 0.2 Angstroms, and underestimated by MP2 by 0.2=20= Angstoms; DFT on the other hand works well with deviations of 0.01 Angstroms or=20 less; [see: M. Swart and J.G. Snijders, Theor. Chem. Acc. 2003 , 110, 34-41=20 (erratum: ibid. 111 , 56)]. Usually for main-group elements, the difference between MP2 and Gx=20 theories is not that dramatic, so draw your conclusions about the accuracy of composite Gx theories=20 for transition metal complexes. =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E m.swart_-_few.vu.nl W http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 Starting May 1, 2006: ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-19--974390893 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 On Friday, January 27, 2006, at 01:00 AM, Young Leh youngleh-#-gmail.com wrote: I have been collecting information on the application of composite energy methods to transition metals for a long time. All the popular composite energy methods, Gaussian-n, Complete Basis Set, and multi-coefficent, are only calibarited with first, second, and third row elements excluding transition metals. Is there any composite energy method that can be applied to transition metal at all? Or if I am going to use those methods to transition metals, how wrong could I be? Probably very wrong, because the transition metals are in a league of their own; see for instance the following paper for a systematic study on the performance of DFT functionals for spin state energies (note: spin state energies are even more difficult than "regular" energies): FuturaJ. Phys. Chem. A Futura2004 Futura,108 , 5479-5483=20 M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma=20 "Validation of exchange-correlation functionals for spin states of iron-complexes"=20 Note also that for instance for ferrocene, the Fe-ring distance is overestimated by RHF by 0.2 Angstroms, and underestimated by MP2 by 0.2 Angstoms;=20 DFT on the other hand works well with deviations of 0.01 Angstroms or less; [see: M. Swart and J.G. Snijders, Theor. Chem. Acc. 2003 , 110, 34-41 (erratum: ibid. 111 , 56)]. Usually for main-group elements, the difference between MP2 and Gx theories is not that dramatic, so draw your conclusions about the accuracy of composite Gx theories for transition metal complexes. = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96 Courierdr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E = 1919,1919,FFFFm.swart_-_few.vu.nl W=20 = 1919,1919,FFFFhttp://www.few.vu.nl/~swart= = Helvetica=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96 = Courier0000,= 4040,8080Starting May 1, 2006: = Courier0000,4040,8080 ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) = Helvetica000= 0,4040,8080=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= --Apple-Mail-19--974390893-- From owner-chemistry@ccl.net Sat Jan 28 00:50:02 2006 From: "Marcel Swart m.swart^few.vu.nl" To: CCL Subject: CCL:G: composite energy method with transition metal Message-Id: <-30671-060127160019-28031-UfkgLw0gPYi/nBhRb7yUsA]^[server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-14--975217394 Date: Fri, 27 Jan 2006 21:20:56 +0100 Mime-Version: 1.0 (Apple Message framework v553) Sent to CCL by: Marcel Swart [m.swart[*]few.vu.nl] --Apple-Mail-14--975217394 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed On Friday, January 27, 2006, at 01:00 AM, Young Leh=20 youngleh-#-gmail.com wrote: > I have been collecting information on the application of composite=20 > energy methods to transition metals for a long time. All the popular=20= > composite energy methods, Gaussian-n, Complete Basis Set, and=20 > multi-coefficent, are only calibarited with first, second, and third=20= > row elements excluding transition metals. Is there any composite=20 > energy method that can be applied to transition metal at all? Or if I=20= > am going to use those methods to transition metals, how wrong could I=20= > be? Probably very wrong, because the transition metals are in a league of=20 their own; see for instance the following paper for a systematic study on the=20 performance of DFT functionals for spin state energies (note: spin state energies are=20= even more difficult than "regular" energies): J. Phys. Chem. A 2004 ,108 , 5479-5483 M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma "Validation of exchange-correlation functionals for spin states of=20 iron-complexes" Note also that for instance for ferrocene, the Fe-ring distance is overestimated by RHF by 0.2 Angstroms, and underestimated by MP2 by 0.2=20= Angstoms; DFT on the other hand works well with deviations of 0.01 Angstroms or=20 less; [see: M. Swart and J.G. Snijders, Theor. Chem. Acc. 2003 , 110, 34-41=20 (erratum: ibid. 111 , 56)]. Usually for main-group elements, the difference between MP2 and Gx=20 theories is not that dramatic, so draw your conclusions about the accuracy of composite Gx theories=20 for transition metal complexes. =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E m.swart###few.vu.nl W http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 Starting May 1, 2006: ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-14--975217394 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 On Friday, January 27, 2006, at 01:00 AM, Young Leh youngleh-#-gmail.com wrote: I have been collecting information on the application of composite energy methods to transition metals for a long time. All the popular composite energy methods, Gaussian-n, Complete Basis Set, and multi-coefficent, are only calibarited with first, second, and third row elements excluding transition metals. Is there any composite energy method that can be applied to transition metal at all? Or if I am going to use those methods to transition metals, how wrong could I be? Probably very wrong, because the transition metals are in a league of their own; see for instance the following paper for a systematic study on the performance of DFT functionals for spin state energies (note: spin state energies are even more difficult than "regular" energies): FuturaJ. Phys. Chem. A Futura2004 Futura,108 , 5479-5483=20 M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma=20 "Validation of exchange-correlation functionals for spin states of iron-complexes"=20 Note also that for instance for ferrocene, the Fe-ring distance is overestimated by RHF by 0.2 Angstroms, and underestimated by MP2 by 0.2 Angstoms;=20 DFT on the other hand works well with deviations of 0.01 Angstroms or less; [see: M. Swart and J.G. Snijders, Theor. Chem. Acc. 2003 , 110, 34-41 (erratum: ibid. 111 , 56)]. Usually for main-group elements, the difference between MP2 and Gx theories is not that dramatic, so draw your conclusions about the accuracy of composite Gx theories for transition metal complexes. = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96 Courierdr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E = 1919,1919,FFFFm.swart###few.vu.nl W=20 = 1919,1919,FFFFhttp://www.few.vu.nl/~swart= = Helvetica=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96 = Courier0000,= 4040,8080Starting May 1, 2006: = Courier0000,4040,8080 ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) = Helvetica000= 0,4040,8080=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= --Apple-Mail-14--975217394-- From owner-chemistry@ccl.net Sat Jan 28 10:17:00 2006 From: "b wafaa wafaab2(_)yahoo.fr" To: CCL Subject: CCL:G: localisation of transition states with gaussian Message-Id: <-30672-060128064625-19230-pFAm+HJLwztDhjGRx1Kxog[]server.ccl.net> X-Original-From: b wafaa Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2071525535-1138445180=:27426" Date: Sat, 28 Jan 2006 11:46:20 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: b wafaa [wafaab2(_)yahoo.fr] --0-2071525535-1138445180=:27426 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I am studing cycloaddition (Diels-alder, 1,3 dipolar) reactions using theoretical approaches and I find great difficulties to locate transition states when bulk substituents (phenyl groups) are present in the reagents. I use the options: B3LYP/6-31G(d) Opt(TS, Noeigentest, Maxcycle=500) freq . However, the convergence fails after 2 or 3 days of calculation ?. I need your help for overcoming this problem if you have ideas about other options or astutenesses available in gaussian 98W software. Thank you in advance. W. Benchouk Melle Wafaa BENCHOUK Laboratoire de Chimie Théorique et modélisation Moléculaire Département de Chimie, Faculté des Sciences, Université A. Belkaid de Tlemcen, B.P. 119,Tlemcen, 13000, ALGERIA Tél: + 213 43 28 63 49 poste 229 Fax: + 213 43 28 61 08 e-mail: benchouk_wafaa/a\yahoo.fr --------------------------------- Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta. --0-2071525535-1138445180=:27426 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCLers,
I am studing cycloaddition (Diels-alder, 1,3 dipolar) reactions using theoretical approaches and I find great difficulties to locate transition states when bulk substituents (phenyl groups) are present in the reagents. 
I use the options:   B3LYP/6-31G(d) Opt(TS, Noeigentest, Maxcycle=500) freq . However, the convergence fails after 2 or 3 days of calculation ?.
I need your help for overcoming this problem if you have ideas about other options or astutenesses available in gaussian 98W software.
Thank you in advance.
W. Benchouk


Melle Wafaa BENCHOUK
Laboratoire de Chimie Théorique et modélisation Moléculaire
Département de Chimie, Faculté des Sciences,
Université A. Belkaid de Tlemcen, B.P. 119,Tlemcen, 13000, ALGERIA
Tél: + 213 43 28 63 49 poste 229
Fax: + 213 43 28 61 08
e-mail: benchouk_wafaa/a\yahoo.fr

Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez la version beta. --0-2071525535-1138445180=:27426-- From owner-chemistry@ccl.net Sat Jan 28 10:52:00 2006 From: "Colette FOULIE foulie.colette**wanadoo.fr" To: CCL Subject: CCL: normal modes Message-Id: <-30673-060128031823-16424-OoIpRCYDyQjqxEv0hjNetg(~)server.ccl.net> X-Original-From: "Colette FOULIE" Sent to CCL by: "Colette FOULIE" [foulie.colette,,wanadoo.fr] Hi CCLers, I would like to calculate the normal modes of few proteins with CHARMm. I have read the vibran.doc in the CHARMm web page but the syntax is not clear for me. Does anybody can tell me the correct syntax ? Moreover, with which tool and how can I use theses normal modes ? Thanks in advance, Colette FOULIE From owner-chemistry@ccl.net Sat Jan 28 11:35:02 2006 From: "Mark Zottola mzottola * gmail.com" To: CCL Subject: CCL:G: AMSOL Question Message-Id: <-30674-060128112358-17004-w/8woSZc9t4otrb+srIBSQ * server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary="----=_Part_11700_8950891.1138462191404" Date: Sat, 28 Jan 2006 10:29:51 -0500 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola||gmail.com] ------=_Part_11700_8950891.1138462191404 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I am exploring the behaviour of a modestly-sized molecule in water. As the PCM models for water are known to fail to account for charge transfer, the other ab initio method would be to include a solvation shell. As this molecule would require approximately 10 waters, I would like to get an initial answer much quicker than ab initio methods on such a system would allow. Since AMSOL is parameterized to account for charge transfer, etc., it seems the obvious choice to answer my questions. To that end, I have a few unresolved questions after reading the AMSOL manual: 1) How does one build the z-matrix format that is used in AMSOL? This is not the traditional z-matrix form used in Gaussian. I can build a z-matrix - the question is how does one build an AMSOL z-matrix? 2) There appears to be a vicious circle in the creation of an AMSOL input deck. The input deck requires charges from an AMSOL run in order to run th= e calculation. How does one get AMSOL charges before running an AMSOL job? = I am sure I am misunderstanding the situation, but not sure where my mis-understanding arises. Thanks for your help! Mark ------=_Part_11700_8950891.1138462191404 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
I am exploring the behaviour of a modestly-sized molecule in water.&nb= sp; As the PCM models for water are known to fail to account for charge tra= nsfer, the other ab initio method would be to include a solvation shell.&nb= sp; As this molecule would require approximately 10 waters, I would like to= get an initial answer much quicker than ab initio methods on such a system= would allow.  Since AMSOL is parameterized to account for charge tran= sfer, etc., it seems the obvious choice to answer my questions.
 
To that end, I have a few unresolved questions after reading the AMSOL= manual:
 
1)  How does one build the z-matrix format that is used in AMSOL?=   This is not the traditional z-matrix form used in Gaussian.  I = can build a z-matrix - the question is how does one build an AMSOL z-matrix= ?
 
2)  There appears to be a vicious circle in the creation of an AM= SOL input deck.  The input deck requires charges from an AMSOL run in = order to run the calculation.  How does one get AMSOL charges before r= unning an AMSOL job?  I am sure I am misunderstanding the situation, b= ut not sure where my mis-understanding arises. =20
 
Thanks for your help!
 
 
Mark
------=_Part_11700_8950891.1138462191404-- From owner-chemistry@ccl.net Sat Jan 28 14:58:00 2006 From: "Chaitanya Krishna A icymist82(0)yahoo.com" To: CCL Subject: CCL: Monte Carlo Codes or Software Message-Id: <-30675-060128122857-12356-Kr20jGp+aWmT3wIi3h8WRQ.@.server.ccl.net> X-Original-From: Chaitanya Krishna A Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 28 Jan 2006 09:28:51 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Chaitanya Krishna A [icymist82=yahoo.com] Hi, That's the one. Thanks for writing. Thanks for bringing the others to my notice. Regards, Chaitanya. --- "Anthony Fejes fejes|,|zymeworks.com" wrote: > Sent to CCL by: Anthony Fejes [fejes _ zymeworks.com] > > The MC suite you're thinking about, with a bird as a logo is probably > MCCCS Towhee: > > http://towhee.sourceforge.net/ > > Cheers > > > After some googling I came across BOSS. Acutally I know of a Monte Carlo > suite > > with a bird as their logo. Now I forgot which. If any one of you knows > about > > it, kindly let me know. > > > > Regards, > > Chaitanya. > > -- > Anthony Fejes > Zymeworks Inc. - A Catalyst in Design > > 201-1401 West Broadway Ave, > Vancouver, B.C. > Canada, V6H 1H6 > > www.zymeworks.com> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Jan 28 15:33:00 2006 From: "David M. Close closed~!~etsu.edu" To: CCL Subject: CCL: OPT on large molecules Message-Id: <-30676-060128114134-23904-G/lCIBhelCnhYTrCfJ2zGA%%server.ccl.net> X-Original-From: "David M. Close" Sent to CCL by: "David M. Close" [closed(_)etsu.edu] CCLers: I have a question about the necessity of optimizations. I have uncovered an effect experimentally that involves changes in large molecules. By large I mean that even partial optimizations with modest basis sets take several days. The effect involves charge migration from one region of the molecule to another region. I would like to examine this effect with computations. After a weeks work I still don't have an answer because of the times taken to determine the optimized structures. I realize that the correct approach is to do calculations on the optimized structures. For example, it is necessary to do frequency calculations on the optimized structures using the same basis sets in both calculations. But what if one didn't use the optimized structures? Suppose one only used a good guess at the optimized structure? Would this cause the later calculations to be invalid? Or might they be good enough to at least decide if the effect of interest is present and that actual optimizations are worthwhile? Regards, Dave Close. From owner-chemistry@ccl.net Sat Jan 28 16:07:00 2006 From: "Warren DeLano warren.:.delsci.com" To: CCL Subject: CCL: Current Stereo 3D Display Info Message-Id: <-30677-060128145719-26240-/jgHoIzzWk9UoKMjo01e8g|-|server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 28 Jan 2006 11:59:04 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren(-)delsci.com] Folks, Whether you favor Macintosh, Linux, or Windows for stereo 3D visualization, you're going to need some specific (and increasingly rare) hardware. To help you find it, we've just updated our information page on stereo-3D-capable displays, cards, emitters, and glasses: http://pymol.sf.net/stereo3d.html Remarkably, we can now only find one company selling a brand new CRT monitor suitable for stereo 3D. If you find any others, please do let us know! Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren:_:delsci.com From owner-chemistry@ccl.net Sat Jan 28 17:06:00 2006 From: "Yingbin Ge yingbin.ge:+:gmail.com" To: CCL Subject: CCL: OPT on large molecules Message-Id: <-30678-060128170451-32662-N7CdpzYbA2BowA1QP3ZusQ _ server.ccl.net> X-Original-From: Yingbin Ge Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 28 Jan 2006 16:04:40 -0600 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge[]gmail.com] Hi David, It depends on the shape of the potential energy surface (PES). If the structure has a bumpy PES, you may get ridiculous vib frequencies even if the coordinates are very close to the optimized ones. Yingbin On 1/28/06, David M. Close closed~!~etsu.edu wrote: > Sent to CCL by: "David M. Close" [closed(_)etsu.edu] > CCLers: > I have a question about the necessity of optimizations. I have uncovered > an effect experimentally that involves changes in large molecules. By large I mean that even partial optimizations with modest basis sets take several days. The effect involves charge migration from one region of the molecule to another region. I would like to examine this effect with computations. After a weeks work I still don't have an answer because of the times taken to determine the optimized structures. > I realize that the correct approach is to do calculations on the optimized structures. For example, it is necessary to do frequency calculations on the optimized structures using the same basis sets in both calculations. But what if one didn't use the optimized structures? Suppose one only used a good guess at the optimized structure? Would this cause the later calculations to be invalid? Or might they be good enough to at least decide if the effect of interest is present and that actual > optimizations are worthwhile? > Regards, Dave Close.> > > > From owner-chemistry@ccl.net Sat Jan 28 19:41:00 2006 From: "Jim Kress ccl_nospam[A]kressworks.com" To: CCL Subject: CCL:G: AMSOL Question Message-Id: <-30679-060128174851-29442-BSDSlnEqxCT3EIxdhbCpRw^_^server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 28 Jan 2006 14:44:42 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam|*|kressworks.com] Why don't you try the Fragment Method in GAMESS/ PCGAMESS? It was specifically designed for system such as yours. Jim > -----Original Message----- > From: Mark Zottola mzottola * gmail.com > [mailto:owner-chemistry(a)ccl.net] > Sent: Saturday, January 28, 2006 11:49 AM > To: Kress, Jim > Subject: CCL:G: AMSOL Question > > Sent to CCL by: Mark Zottola [mzottola||gmail.com] > ------=_Part_11700_8950891.1138462191404 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > I am exploring the behaviour of a modestly-sized molecule in > water. As the PCM models for water are known to fail to > account for charge transfer, the other ab initio method would > be to include a solvation shell. As this molecule would > require approximately 10 waters, I would like to get an > initial answer much quicker than ab initio methods on such a > system would allow. Since AMSOL is parameterized to account > for charge transfer, etc., it seems the obvious choice to > answer my questions. > > To that end, I have a few unresolved questions after reading the AMSOL > manual: > > 1) How does one build the z-matrix format that is used in > AMSOL? This is not the traditional z-matrix form used in > Gaussian. I can build a z-matrix > - the question is how does one build an AMSOL z-matrix? > > 2) There appears to be a vicious circle in the creation of > an AMSOL input deck. The input deck requires charges from an > AMSOL run in order to run th= e calculation. How does one > get AMSOL charges before running an AMSOL job? = I am sure I > am misunderstanding the situation, but not sure where my > mis-understanding arises. > > Thanks for your help! > > > Mark > > ------=_Part_11700_8950891.1138462191404 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > >
I am exploring the behaviour of a modestly-sized > molecule in water.&nb= sp; As the PCM models for water are > known to fail to account for charge tra= nsfer, the other ab > initio method would be to include a solvation shell.&nb= sp; > As this molecule would require approximately 10 waters, I > would like to= get an initial answer much quicker than ab > initio methods on such a system= would allow.  Since > AMSOL is parameterized to account for charge tran= sfer, > etc., it seems the obvious choice to answer my questions. >
>
 
>
To that end, I have a few unresolved questions after > reading the AMSOL= manual:
 
>
1)  How does one build the z-matrix format that is > used in AMSOL?=   This is not the traditional z-matrix > form used in Gaussian.  I = can build a z-matrix - the > question is how does one build an AMSOL z-matrix= ?
>
 
2)  There appears to be a vicious > circle in the creation of an AM= SOL input deck.  The > input deck requires charges from an AMSOL run in = order to > run the calculation.  How does one get AMSOL charges > before r= unning an AMSOL job?  I am sure I am > misunderstanding the situation, b= ut not sure where my > mis-understanding arises. =20
 
>
Thanks for your help!
 
>
 
Mark
> > ------=_Part_11700_8950891.1138462191404-- > > > > -= 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 (a) sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Sat Jan 28 20:42:00 2006 From: "Don Steiger sd00_2002::yahoo.com" To: CCL Subject: CCL: MD software question. Message-Id: <-30680-060128171959-19891-vbSareQRVtiW0lqYll/27A/a\server.ccl.net> X-Original-From: "Don Steiger" Sent to CCL by: "Don Steiger" [sd00_2002[-]yahoo.com] I have an MD question. As far as I can tell, the equations/math that goes into MD are fairly straight forward and short. Yet there are a lot of MD packages, and all of them are very large. So what is in these packages that makes them so large?