From owner-chemistry@ccl.net Tue Mar 13 05:32:01 2012 From: "Frank Neese neese]|[mpi-muelheim.mpg.de" To: CCL Subject: CCL: CASSCF does not produce spin densities Message-Id: <-46470-120313045707-10917-+Py7MxAF1EMDx/g+3f8dnQ#server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 13 Mar 2012 09:56:58 +0100 Mime-Version: 1.0 (Apple Message framework v1257) Sent to CCL by: Frank Neese [neese_._mpi-muelheim.mpg.de] Dear Joseph, there definitely is a spin density associated with a CASSCF wave function as long as the total spin is larger than 0. It would be a major misconception to think that spin-density only arises in a spin unrestricted framework. I don't know about other programs, but at least the ORCA program will print spin populations following a CASSCF calculation (please note that there is a distinct difference between the spin density=a three dimensional function of space and the spin-population= are more or less well justified distribution of the spin density onto individual atoms) and also calculate expectation values such as isotropic and dipolar hyperfine couplings on the basis of the spin density. However, CASSCF is a Hartree-Fock level method - definitely not a high level treatment. In my humble opinion, it is unlikely to produce accurate results for iron-nitrosyl systems that are notoriously difficult. In particular, it will not do well on isotropic hyperfine couplings as these require a proper treatment of spin-polarization which you will not achieve at the CASSCF level. It only properly comes into play once you include certain classes of double excitations on top of the CASSCF reference wavefunction and also take them into account in evaluating the density. I hope that helps a bit?! Best regards, Frank Am 12.03.2012 um 18:37 schrieb Joseph Katigbak jkatigba/./stevens.edu: > > Sent to CCL by: "Joseph Katigbak" [jkatigba{:}stevens.edu] > Hello, I am trying to determine the hyperfine coupling constants of some > nitrosyl compounds using a high level Multiconfigurational/Multireference > method like CASSCF. After running a CAS calculation using ROHF molecular > orbitals as guesses, I got energy convergence for my compounds. However i > noticed that the spin densities weren't being printed out (I was looking > specifically for the Isotropic Fermi contact coupling). I have been told that > CASSCF implements a restricted SCF colution and therefore does not generate a > spin density. However I know from the literature that there are several papers > on iron nitrosyl systems that use CASSCF and have spin densities. Is there any > way for me to get the spin densities/Fermi contact coupling term? or am i just > doing it wrong? > > > Thank you very much :D > -J. Katigbak> > > From owner-chemistry@ccl.net Tue Mar 13 08:37:00 2012 From: "Georg Lefkidis lefkidis!A!physik.uni-kl.de" To: CCL Subject: CCL:G: AW: CASSCF does not produce spin densities Message-Id: <-46471-120313083620-26296-aQUa0IikKpJmmXOjpmUtZw~!~server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 13 Mar 2012 13:36:10 +0100 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis^^physik.uni-kl.de] Dear Josehp, with all respect, but Frank Neese's statement is wrong. CASSCF is a post-HF, multi-determinental, configuration-interaction method (it is a multireference method [look e.g. in Chem. Phys. Lett., 93 (1982) 43-46, Chem. Phys. Lett., 83 (1981) 362-68 ]). It provides wavefunctions which are linear combinations of Slater determinants, and in fact is one of the best methods around to calculate static correlations. The reason is that it not only optimizes the coefficients of the determinental expansion but also the MO themselves (look for STATEAVERAGE in Gaussian). In fact it provides excellent results for transition metal elements (I myself have several publications using CASSCF). Unfortunately Gaussian's output is somehow cryptic, in that it produces the new optimized reference HF but it takes some digging to find out the CI coefficients (but they are definitely there - results, by the way, are calculated from the complete, internally stored density matrix and not the simple HF output). It is true however that it provides not (or very poor) spin-polarization results (SOC or hyperfine splitting). As for the spin polarization, I personally calculate it on top of Gaussian's results by extracting the complete wavefunction. It is indeed a very tedious procedure, but surely possible. Best regards Georg -----Ursprüngliche Nachricht----- Von: owner-chemistry+lefkidis==physik.uni-kl.de^ccl.net [mailto:owner-chemistry+lefkidis==physik.uni-kl.de^ccl.net] Im Auftrag von Frank Neese neese]|[mpi-muelheim.mpg.de Gesendet: Dienstag, 13. März 2012 09:57 An: Lefkidis, Georg Betreff: CCL: CASSCF does not produce spin densities Sent to CCL by: Frank Neese [neese_._mpi-muelheim.mpg.de] Dear Joseph, there definitely is a spin density associated with a CASSCF wave function as long as the total spin is larger than 0. It would be a major misconception to think that spin-density only arises in a spin unrestricted framework. I don't know about other programs, but at least the ORCA program will print spin populations following a CASSCF calculation (please note that there is a distinct difference between the spin density=a three dimensional function of space and the spin-population= are more or less well justified distribution of the spin density onto individual atoms) and also calculate expectation values such as isotropic and dipolar hyperfine couplings on the basis of the spin density. However, CASSCF is a Hartree-Fock level method - definitely not a high level treatment. In my humble opinion, it is unlikely to produce accurate results for iron-nitrosyl systems that are notoriously difficult. In particular, it will not do well on isotropic hyperfine couplings as these require a proper treatment of spin-polarization which you will not achieve at the CASSCF level. It only properly comes into play once you include certain classes of double excitations on top of the CASSCF reference wavefunction and also take them into account in evaluating the density. I hope that helps a bit?! Best regards, Frank Am 12.03.2012 um 18:37 schrieb Joseph Katigbak jkatigba/./stevens.edu: > > Sent to CCL by: "Joseph Katigbak" [jkatigba{:}stevens.edu] Hello, I > am trying to determine the hyperfine coupling constants of some > nitrosyl compounds using a high level > Multiconfigurational/Multireference > method like CASSCF. After running a CAS calculation using ROHF > molecular orbitals as guesses, I got energy convergence for my > compounds. However i noticed that the spin densities weren't being > printed out (I was looking specifically for the Isotropic Fermi > contact coupling). I have been told that CASSCF implements a > restricted SCF colution and therefore does not generate a spin > density. However I know from the literature that there are several > papers on iron nitrosyl systems that use CASSCF and have spin > densities. Is there any way for me to get the spin densities/Fermi contact coupling term? or am i just doing it wrong? > > > Thank you very much :D > -J. Katigbakhttp://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 Tue Mar 13 09:45:01 2012 From: "Jim Kress ccl_nospam[]kressworks.com" To: CCL Subject: CCL: CASSCF does not produce spin densities Message-Id: <-46472-120313090945-8540-kyJe7hz6ym7FwcSR9wxRNw\a/server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 Mar 2012 09:09:20 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam~!~kressworks.com] It would be helpful to know what software you are using and what software was being used in the papers you referenced. Also, the input information you provided to your software package would also be useful information to determine if there was need for additional specification of keywords to acquire the information you seek. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com,,ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com,,ccl.net] On Behalf > Of Joseph Katigbak jkatigba/./stevens.edu > Sent: Monday, March 12, 2012 1:37 PM > To: Kress, Jim > Subject: CCL: CASSCF does not produce spin densities > > > Sent to CCL by: "Joseph Katigbak" [jkatigba{:}stevens.edu] Hello, I am trying > to determine the hyperfine coupling constants of some nitrosyl compounds > using a high level Multiconfigurational/Multireference > method like CASSCF. After running a CAS calculation using ROHF molecular > orbitals as guesses, I got energy convergence for my compounds. However i > noticed that the spin densities weren't being printed out (I was looking > specifically for the Isotropic Fermi contact coupling). I have been told that > CASSCF implements a restricted SCF colution and therefore does not > generate a spin density. However I know from the literature that there are > several papers on iron nitrosyl systems that use CASSCF and have spin > densities. Is there any way for me to get the spin densities/Fermi contact > coupling term? or am i just doing it wrong? > > > Thank you very much :D > -J. KatigbakTo > 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 look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Tue Mar 13 10:28:01 2012 From: "Alcides Simao alsimao*o*gmail.com" To: CCL Subject: CCL: Ring Pseudorotation Message-Id: <-46473-120313102635-6118-wElncviwhH7THo3GOwCfhA ~~ server.ccl.net> X-Original-From: Alcides Simao Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 13 Mar 2012 14:26:24 +0000 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao ~ gmail.com] Dear All, I would like to thank you all for the wealth of information provided regarding this problem. Your help proved invaluable! Also, I must say that I found it quite interesting that people find the word 'automagic' funny. I learned this world by reading some scripts from an old friend of mine, who, long time ago, was my teacher in the Computational Chemistry and cultivated my passion for Linux. Cheers, Paulo! ;) So, again, thank you all! > From a dark pit somewhere in continental Europe, Alcides From owner-chemistry@ccl.net Tue Mar 13 11:03:01 2012 From: "Nuno A. G. Bandeira nuno.bandeira/./ist.utl.pt" To: CCL Subject: CCL:G: AW: CASSCF does not produce spin densities Message-Id: <-46474-120313101708-31094-6sf86EDJXnJ6JI0ARq/now+/-server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 13 Mar 2012 14:16:58 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira#%#ist.utl.pt] On 13-03-2012 12:36, Georg Lefkidis lefkidis!A!physik.uni-kl.de wrote: > Sent to CCL by: "Georg Lefkidis" [lefkidis^^physik.uni-kl.de] > Dear Josehp, > > with all respect, but Frank Neese's statement is wrong. CASSCF is a post-HF, > multi-determinental, configuration-interaction method (it is a > multireference method [look e.g. in Chem. Phys. Lett., 93 (1982) 43-46, > Chem. Phys. Lett., 83 (1981) 362-68 ]). It provides wavefunctions which are > linear combinations of Slater determinants, and in fact is one of the best > methods around to calculate static correlations. The reason is that it not > only optimizes the coefficients of the determinental expansion but also the > MO themselves (look for STATEAVERAGE in Gaussian). In fact it provides > excellent results for transition metal elements (I myself have several > publications using CASSCF). I'm sorry but this statement is just wrong. CASSCF deals with static correlations but not dynamical correlation unless the active space tends to infinity. If this were true there would be no need for higher level treatments like CASPT2, MRMP2, CASMP2 and the like and the literature dealing with transition metal complexes is riddled with such methods exactly because the dynamical correlation issue is far more frequent and far more critical than static correlation. A mere singlet triplet gap cannot be computed by CASSCF alone because the active space window does not account for how the rest of the electrons interact with the active space and vice-versa. I'm glad that you are brave enough to face referees with mere CASSCF calculations. I imagine that there are still people that do HF calculations too. But these days they cannot be taken too seriously. -- Nuno A. G. Bandeira, AMRSC -- From owner-chemistry@ccl.net Tue Mar 13 11:54:01 2012 From: "Laidig, Bill laidig.wd__pg.com" To: CCL Subject: CCL: PCA using JMP from Amber .dat files Message-Id: <-46475-120313082335-14218-16wVILViOUP8pmZScsGJ0g=server.ccl.net> X-Original-From: "Laidig, Bill" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 Mar 2012 12:23:28 +0000 MIME-Version: 1.0 Sent to CCL by: "Laidig, Bill" [laidig.wd]![pg.com] I would read them into Excel, add header lines and then copy from Excel to JMP (this is typically how I get data into JMP). Bill -----Original Message----- > From: owner-chemistry+laidig.wd==pg.com~!~ccl.net [mailto:owner-chemistry+laidig.wd==pg.com~!~ccl.net] On Behalf Of Kira A Armacost kza0004#%#auburn.edu Sent: Monday, March 12, 2012 3:33 PM To: Laidig, Bill Subject: CCL: PCA using JMP from Amber .dat files Sent to CCL by: "Kira A Armacost" [kza0004=auburn.edu] I'm trying to perform PCA using ptraj in Amber Tools from Amber 11. I've been able to get a .dat file with the eigenvectors and eigenvalues. I am wondering if these .dat files can be uploaded into JMP for further use with PCA? I'm able to upload them, but am running into an error with jmp because there is no headline for each column from the .dat file. Thank you!http://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 Tue Mar 13 12:29:00 2012 From: "Ranjita Das ranjitadas.85() gmail.com" To: CCL Subject: CCL: Problem with DKH calculation Message-Id: <-46476-120313100924-25486-J6a86/9Zlre9zqGUS4Gmrg/./server.ccl.net> X-Original-From: "Ranjita Das" Date: Tue, 13 Mar 2012 10:09:22 -0400 Sent to CCL by: "Ranjita Das" [ranjitadas.85.:.gmail.com] Hi, I am trying to do Douglas-Kroll-Hess calculation using G09. My system contains 33 atoms those are C, N, H and oly one Ti atom. I am trying to optimize the system using DKH calculation, in input I have used the command # B3LYP Gen Integral=DKH2 IOP(3/93=2) opt freq {title} {charge}, {multiplicity} {coordinates} {basis sets} but always i get the following error message ************************************************ ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** ************************************************ Error termination via Lnk1e in /opt/g09/l114.exe at Tue Mar 13 07:20:22 2012. Job cpu time: 0 days 0 hours 0 minutes 1.1 seconds. File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1 please help me. Thanks Ranjita From owner-chemistry@ccl.net Tue Mar 13 13:04:00 2012 From: "Neese, Frank frank.neese{:}mpi-mail.mpg.de" To: CCL Subject: CCL: CASSCF does not produce spin densities Message-Id: <-46477-120313112613-31617-sEo9U1YrRJLv35gVXaz5Kg^^^server.ccl.net> X-Original-From: "Neese, Frank" Content-Language: en-US Content-Type: multipart/signed; boundary="Apple-Mail=_52BF2114-BEFA-4CC2-A0C9-F559F16EF5A6"; protocol="application/pkcs7-signature"; micalg=sha1 Date: Tue, 13 Mar 2012 16:26:06 +0100 MIME-Version: 1.0 Sent to CCL by: "Neese, Frank" [frank.neese-x-mpi-mail.mpg.de] --Apple-Mail=_52BF2114-BEFA-4CC2-A0C9-F559F16EF5A6 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 In response to Georg and Jim:=20 >with all respect, but Frank Neese's statement is wrong. it looks like we are opening Pandora's box here :-)=20 I nevertheless take the liberty to disagree with the statement brought = forward by Georg. (Not with the stated facts of course. I do understand = what CASSCF is and having programmed diverse multireference methods over = the years I do claim to have at least some appreciation of = multireference wavefunction theory; I know the Schlegl/Robb papers that = were quoted by Georg; they report a convergence enhancement algorithm = for CASSCF wave functions and an application to a reaction between two = very small molecules, i.e. H2CO --> H2 + CO. Very nice work! But IMHO = these papers do not disprove anything I said).=20 My arguments in favor of stating what I have stated in my previous post = are summarized below:=20 As we all know CASSCF is limited to very few number of active orbitals. = The majority of reseachers who have worked intensely in the field of = multiconfigurational self consistent field theory agree that this type = of wavefunction is not meant to cover dynamic correlation which is what = would be required to really go beyond Hartree-Fock level accuracy. = Compared to, say, a closed shell or ROHF CASSCF obviously does include a = tiny amount of dynamic correlation (unless your active space is = trivially small and reduces to the closed shell or ROHF determinant). = However, that tiny little bit of dynamic correlation is essentially = irrelevant. What CASSCF is designed to do is to generalize the = Hartree-Fock method to cases where the single determinant Ansatz is = qualitatively wrong. There are many papers by eminent researchers like = Peter Pulay or Jean Paul Malrieu who state that it would be an abuse of = the CASSCF method to want to cover more than the essential model space = (which is the minimal active space that is needed to cover the static = correlation; that again can mean many things. Sometimes it means = ensuring that your dissociation limit is correctly represented. = Obviously here is where ones chemical thinking comes in). I personally = agree with this reasoning. It is then logical to state that CASSCF is = not a high level method because its accuracy will be similar to that of, = say, RHF in the cases where a closed shell determinant is reasonable. = Thus, CASSCF is of broader applicability (even much broader) and it is = more consistent than R(O)HF, but it is not of strikingly higher accuracy = - provided one compares apples with apples and oranges with oranges. =20 Of course if one defines anything that has more than one determinant as = a post Hartree-Fock method then, yes, there is no doubt that CASSCF is = post-HF. It is not, however, my favorite definition of what a post-HF = method is designed to be. I would tend to use this term if it is implied = that a substantial fraction of the (basis set) dynamic correlation = energy is recovered by the treatment (what is meant by "dynamic = correlation" is, again, a matter of the reference point. If you argue = > from a multireference perturbation theory or multireference = configuration interaction or multireference coupled cluster point of = view then CASSCF is the starting point and does not contain dynamic = correlation).=20 At the end of the day everybody is of course free to do whatever = calculation one wants and maybe one has good reasons for wanting to = cover some dynamic correlation already with a CASSCF wave function. A = typical example is the double d-shell effect for transition metal = calculations in conjunction with the CASSCF/CASPT2 method that in = particular Kristin Pierloot has elaborated on many times (in this case = one covers a radial correlation effect). My personal preference, = however, is to do this with a post-CASSCF treatment (if one can afford = it).=20 We too have had many good results with CASSCF and transition metals. My = concerns were directed at the particular problem that the colleague was = mentioning. Having worked on both, multireference wavefunctions and iron = nitrosyl systems, I have simply expressed concerns to regard CASSCF as a = high level treatment that should be given preference over any other = theoretical method. To do so would, in my opinion, require solid backup = > from comparison of calculated to observed physical properties.=20 The discussion that we have been starting here could very quickly turn = into a hair splitting dispute about terminology and I hope that this is = not what will happen. I have simply tried here to explain what my take = on the subject is and I do, of course, respect any other approach or = opinion that leads to creative and interesting science.=20 Best regards Frank = ------------------------------------------------------------------------- Prof. Dr. Frank Neese - Director - Max-Planck Institut f=FCr Bioanorganische Chemie Stiftstr. 34-36 D-45470 M=FClheim an der Ruhr Germany E-Mail: Frank.Neese ~~ mpi-mail.mpg.de = ------------------------------------------------------------------------- --Apple-Mail=_52BF2114-BEFA-4CC2-A0C9-F559F16EF5A6 Content-Disposition: attachment; filename="smime.p7s" Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIIOVTCCBCEw ggMJoAMCAQICAgDHMA0GCSqGSIb3DQEBBQUAMHExCzAJBgNVBAYTAkRFMRwwGgYDVQQKExNEZXV0 c2NoZSBUZWxla29tIEFHMR8wHQYDVQQLExZULVRlbGVTZWMgVHJ1c3QgQ2VudGVyMSMwIQYDVQQD 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DQEHATAcBgkqhkiG9w0BCQUxDxcNMTIwMzEzMTUyNjA2WjAjBgkqhkiG9w0BCQQxFgQUlVCqapkx IY/3dZ6qFAtESmpP0HoweAYJKwYBBAGCNxAEMWswaTBeMQswCQYDVQQGEwJERTEgMB4GA1UEChMX TWF4LVBsYW5jay1HZXNlbGxzY2hhZnQxDzANBgNVBAMTBk1QRyBDQTEcMBoGCSqGSIb3DQEJARYN bXBnLWNhQG1wZy5kZQIHEvxhlkQFAjB6BgsqhkiG9w0BCRACCzFroGkwXjELMAkGA1UEBhMCREUx IDAeBgNVBAoTF01heC1QbGFuY2stR2VzZWxsc2NoYWZ0MQ8wDQYDVQQDEwZNUEcgQ0ExHDAaBgkq hkiG9w0BCQEWDW1wZy1jYUBtcGcuZGUCBxL8YZZEBQIwDQYJKoZIhvcNAQEBBQAEggEAEyiDNu32 8sUng/MDi+OwQvv+pyDGQcwHDvsww8Qb19ZMlmxPrMlcR8WqZKaZxhE+/e1RRVQT/LHAWWoyXYbK TBF/6ehvqADVtvRXzXYIS785OvQVDNTAcXyyR6DM/Fji35TbE6NYVTD1ghTQmpYRe5cW95hOPga6 9NNbwdcYNes7rVjNQszJbEjHwWbXOuhYEcoOLQ7D8xozwtf2zTwsW52bA+fC7jXT+7XI5Pz3PM5P mMYc6KMpzQvnr+N5XgnqEgG9s0d9k99dNDoaj8CqETOJJV54BGOgtyeYpAMqed9l1cAq3ueZbaSl upB5u0wvBhb13l+tZGQVdLKVRNYVQgAAAAAAAA== --Apple-Mail=_52BF2114-BEFA-4CC2-A0C9-F559F16EF5A6-- From owner-chemistry@ccl.net Tue Mar 13 13:39:00 2012 From: "Edward Holland hollandej*|*Cardiff.ac.uk" To: CCL Subject: CCL:G: Problem with DKH calculation Message-Id: <-46478-120313125313-4147-S5jOet1eALF4GYQDvYxv2w\a/server.ccl.net> X-Original-From: Edward Holland Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 13 Mar 2012 16:53:01 +0000 Mime-Version: 1.0 (Apple Message framework v1257) Sent to CCL by: Edward Holland [hollandej:_:Cardiff.ac.uk] I encountered the exact same error message today. I'm not sure why it happens but for some reason gaussian is expecting a z matrix for coordinate input. The easiest way to fix it is to provide your geom in a z mat. Yours Ed Holland On 13 Mar 2012, at 14:09, Ranjita Das ranjitadas.85() gmail.com wrote: > > Sent to CCL by: "Ranjita Das" [ranjitadas.85.:.gmail.com] > Hi, > > I am trying to do Douglas-Kroll-Hess calculation using G09. My system contains 33 atoms those are C, N, H and oly one Ti atom. I am trying to optimize the system using DKH calculation, in input I have used the command > > # B3LYP Gen Integral=DKH2 IOP(3/93=2) opt freq > > {title} > > {charge}, {multiplicity} > > {coordinates} > > > > {basis sets} > > but always i get the following error message > > > ************************************************ > ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** > ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** > ************************************************ > > > Error termination via Lnk1e in /opt/g09/l114.exe at Tue Mar 13 07:20:22 2012. > Job cpu time: 0 days 0 hours 0 minutes 1.1 seconds. > File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1 > > > please help me. > Thanks > > Ranjita> > From owner-chemistry@ccl.net Tue Mar 13 14:14:01 2012 From: "Vera Cathrine vera.cathrine#%#yahoo.com" To: CCL Subject: CCL:G: G09: ONIOM error: Maximum number of microiterations cycles exceeded! Message-Id: <-46479-120313130031-11043-/7FbA/XPK+YXQN80/Q18LA(-)server.ccl.net> X-Original-From: "Vera Cathrine" Date: Tue, 13 Mar 2012 13:00:30 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine ~ yahoo.com] Hello All, I would like to perform a geometry optimization using ONIOM (QM/MM) method and electronic embedding (EE). To achieve convergence I have first optimized my system using mechanical embedding (ME). The ME optimization terminated normally. Then I tried to optimize the geometry with the same method but with electronic embedding (EE). I am encountering the following error: ONIOM: Microiterations cycle 26 out of a maximum of 25 Maximum number of microiterations cycles exceeded! Terminating job. Error termination via Lnk1e in /usr/local/gaussian/g09/l120.exe at Tue Mar 13 17:17:49 2012. my route section reads as #p oniom(pm3:amber)=embed geom=connectivity opt=(quadmac,maxstep=10,ma xcycle=512) iop(2/15=3) nosymm I also tried to change some default optimization criteria but all failed. I would thank you for any suggestion to fix this error. Best wishes, Vera From owner-chemistry@ccl.net Tue Mar 13 14:48:00 2012 From: "Andrew Voronkov drugdesign*yandex.ru" To: CCL Subject: CCL: question about software for signaling pathways depcition Message-Id: <-46480-120313113343-12285-HP0CKoUl4rmg+QAWQiPD1g-$-server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 13 Mar 2012 19:33:34 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[-]yandex.ru] Dear CCL users, this is probably a bit our of CCL topic, but is anyone aware of free software tools for signaling pathways schemes (like this http://proteinlounge.com/PBTool/ListPathwayThumb.aspx) depicition? I have tested protein lounge, but their trial version is quite limited now and also I would prefer to use something offline if possible. Best regards, Andrew From owner-chemistry@ccl.net Tue Mar 13 15:23:00 2012 From: "tim hockswender timhockswender]_[gmail.com" To: CCL Subject: CCL: PCA using JMP from Amber .dat files Message-Id: <-46481-120313114716-26747-5evXSggXnibZB+3WyvNp+Q[-]server.ccl.net> X-Original-From: tim hockswender Content-Type: multipart/alternative; boundary=f46d04426e9275ef4704bb21c58d Date: Tue, 13 Mar 2012 11:47:07 -0400 MIME-Version: 1.0 Sent to CCL by: tim hockswender [timhockswender**gmail.com] --f46d04426e9275ef4704bb21c58d Content-Type: text/plain; charset=ISO-8859-1 JMP does not need column headers to import a file [open with text import with preview]; perhaps the real issue is the column delimiters. On Mon, Mar 12, 2012 at 3:32 PM, Kira A Armacost kza0004#%#auburn.edu < owner-chemistry~~ccl.net> wrote: > > Sent to CCL by: "Kira A Armacost" [kza0004=auburn.edu] > I'm trying to perform PCA using ptraj in Amber Tools from Amber 11. I've > been able to get a .dat file > with the eigenvectors and eigenvalues. I am wondering if these .dat files > can be uploaded into JMP for > further use with PCA? I'm able to upload them, but am running into an > error with jmp because there is > no headline for each column from the .dat file. > Thank you!> > > --f46d04426e9275ef4704bb21c58d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable JMP does not need column headers to import a file [open with text import wi= th preview]; perhaps the real issue is the column delimiters.

On Mon, Mar 12, 2012 at 3:32 PM, Kira A Armacost kza00= 04#%#auburn.edu <owner-chemistry~~ccl.net> wrote:

Sent to CCL by: "Kira A Armacost" [kza0004=3Dauburn.edu]
I'm trying to perform PCA using ptraj in Amber Tools from Amber 11. I&#= 39;ve been able to get a .dat file
with the eigenvectors and eigenvalues. I am wondering if these .dat files c= an be uploaded into JMP for
further use with PCA? I'm able to upload them, but am running into an e= rror with jmp because there is
no headline for each column from the .dat file.
Thank you!



-=3D This is automatically added to each message by the mailing script =3D-=
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--f46d04426e9275ef4704bb21c58d-- From owner-chemistry@ccl.net Tue Mar 13 16:27:00 2012 From: "Anatoli Korkin a_korkin||yahoo.com" To: CCL Subject: CCL: Updating the software links at ASDN.NET Message-Id: <-46482-120313162629-23995-6Mj04FZzRYxIeYJsYOQxXw#server.ccl.net> X-Original-From: "Anatoli Korkin" Date: Tue, 13 Mar 2012 16:26:21 -0400 Sent to CCL by: "Anatoli Korkin" [a_korkin,yahoo.com] Dear CCLers, Thank you to everybody, who answered on my previous message, regarding the web links to education sources. Another links collection, which should be close to the interests of the CCL community - software sites - is also on due for renewal: http://asdn.net/asdn/links/software.shtml I will gladly acknowledge your and your favorite software sources at this web page. A copy of your email to anatoli.korkin/at/asu.edu will be highly appreciated. Best regards, Anatoli Korkin From owner-chemistry@ccl.net Tue Mar 13 19:56:00 2012 From: "Karen.Green|sanofi.com" To: CCL Subject: CCL: question about software for signaling pathways depcition Message-Id: <-46483-120313152656-32290-kV+a7wlTQwQj6ExW2YdOMw:server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 13 Mar 2012 12:26:46 -0700 MIME-Version: 1.0 Sent to CCL by: [Karen.Green,+,sanofi.com] I haven't tried them myself but here are a few free (I think) pathway diagramming software applications: http://www.pathvisio.org/ http://systems-biology.org/software/celldesigner/ + http://www.pantherdb.org/pathway/ http://ecocyc.org/download.shtml -----Original Message----- > From: owner-chemistry+karen.green==sanofi-aventis.com{=}ccl.net [mailto:owner-chemistry+karen.green==sanofi-aventis.com{=}ccl.net] On Behalf Of Andrew Voronkov drugdesign*yandex.ru Sent: Tuesday, March 13, 2012 8:34 AM To: Green, Karen R&D/US Subject: CCL: question about software for signaling pathways depcition Sent to CCL by: Andrew Voronkov [drugdesign[-]yandex.ru] Dear CCL users, this is probably a bit our of CCL topic, but is anyone aware of free software tools for signaling pathways schemes (like this http://proteinlounge.com/PBTool/ListPathwayThumb.aspx) depicition? I have tested protein lounge, but their trial version is quite limited now and also I would prefer to use something offline if possible. Best regards, Andrewhttp://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 Tue Mar 13 20:31:00 2012 From: "Zork Zou zorkzou%gmail.com" To: CCL Subject: CCL:G: Problem with DKH calculation Message-Id: <-46484-120313195617-28528-vOntKgbH9IhzCLCLAAiPoA(a)server.ccl.net> X-Original-From: Zork Zou Content-Type: multipart/alternative; boundary=00151747be082339d604bb289a0d Date: Tue, 13 Mar 2012 18:56:05 -0500 MIME-Version: 1.0 Sent to CCL by: Zork Zou [zorkzou::gmail.com] --00151747be082339d604bb289a0d Content-Type: text/plain; charset=ISO-8859-1 Hi, The DKH Hamiltonian in Gaussian has no analytical derivatives, so the gradients and Hessians of energy are calculated numerically. In this case you have to specify variables in your coordinates. To the best of my knowledge, only the PARAGAUSS program can calculate analytical 1st and 2nd order derivatives of DKH2. The best choice in Gaussian is ECP. Best, Wenli On Tue, Mar 13, 2012 at 9:09 AM, Ranjita Das ranjitadas.85() gmail.com < owner-chemistry ~~ ccl.net> wrote: > > Sent to CCL by: "Ranjita Das" [ranjitadas.85.:.gmail.com] > Hi, > > I am trying to do Douglas-Kroll-Hess calculation using G09. My system > contains 33 atoms those are C, N, H and oly one Ti atom. I am trying to > optimize the system using DKH calculation, in input I have used the command > > # B3LYP Gen Integral=DKH2 IOP(3/93=2) opt freq > > {title} > > {charge}, {multiplicity} > > {coordinates} > > > > {basis sets} > > but always i get the following error message > > > ************************************************ > ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** > ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** > ************************************************ > > > Error termination via Lnk1e in /opt/g09/l114.exe at Tue Mar 13 07:20:22 > 2012. > Job cpu time: 0 days 0 hours 0 minutes 1.1 seconds. > File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > please help me. > Thanks > > Ranjita> > > --00151747be082339d604bb289a0d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi,

=A0

The DKH Hamiltonian in= Gaussian has no analytical derivatives, so the gradients and Hessians of energy are calcula= ted numerically. In this case you have to specify variables in your coordinates= .

=A0

To the best of my know= ledge, only the PARAGAUSS program can calculate analytical 1st and 2nd order=A0derivatives = of DKH2. The best choice in Gaussian is ECP.

=A0

Best,

Wenli



On Tue, Mar 13, 2012 at 9:09 AM, = Ranjita Das ranjitadas.85() gmail.com <owner-chemistr= y ~~ ccl.net> wrote:

Sent to CCL by: "Ranjita =A0Das" [ranjitadas.85.:.gmail.com]
Hi,

I am trying to do Douglas-Kroll-Hess calculation using G09. My system conta= ins 33 atoms those are C, N, H and oly one Ti atom. I am trying to optimize= the system using DKH calculation, in input I have used the command

# B3LYP Gen Integral=3DDKH2 IOP(3/93=3D2) =A0opt freq

{title}

=A0{charge}, {multiplicity}

{coordinates}



{basis sets}

but always i get the following error message


=A0************************************************
=A0** ERROR IN INITNF. NUMBER OF VARIABLES ( =A00) **
=A0** =A0 INCORRECT (SHOULD BE BETWEEN 1 AND 50) =A0 **
=A0************************************************


=A0Error termination via Lnk1e in /opt/g09/l114.exe at Tue Mar 13 07:20:22 = 2012.
=A0Job cpu time: =A00 days =A00 hours =A00 minutes =A01.1 seconds.
=A0File lengths (MBytes): =A0RWF=3D =A0 =A0 =A05 Int=3D =A0 =A0 =A00 D2E=3D= =A0 =A0 =A00 Chk=3D =A0 =A0 =A01 Scr=3D =A0 =A0 =A01


please help me.
Thanks

Ranjita



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--00151747be082339d604bb289a0d-- From owner-chemistry@ccl.net Tue Mar 13 21:06:00 2012 From: "Cory Pye cpye!=!ap.smu.ca" To: CCL Subject: CCL:G: Problem with DKH calculation Message-Id: <-46485-120313210052-32393-F8MrUIawu1/bKScXRlizng_-_server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 13 Mar 2012 22:10:00 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye[*]ap.smu.ca] On Tue, 13 Mar 2012, Ranjita Das ranjitadas.85() gmail.com wrote: > > Sent to CCL by: "Ranjita Das" [ranjitadas.85.:.gmail.com] > Hi, > > I am trying to do Douglas-Kroll-Hess calculation using G09. My system contains 33 atoms those are C, N, H and oly one Ti atom. I am trying to optimize the system using DKH calculation, in input I have used the command > > # B3LYP Gen Integral=DKH2 IOP(3/93=2) opt freq > > {title} > > {charge}, {multiplicity} > > {coordinates} > > > > {basis sets} > > but always i get the following error message > > > ************************************************ > ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** > ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** > ************************************************ > > Hello, this looks like the error you have when you have too many variables in an eigenvector-following method. My hunch is: You have specified the DKH Hamiltonian. Possibly, analytic forces are not available for this method, so the system defaults to an energy only optimization using the eigenvector following method. You have 33 atoms, and therefore 93 degrees of freedom in the absence of symmetry. The limit for the EF method is 50 variables, hence the error. Workarounds: (1) preoptimize without using DHK, do single points with. Another option might be to change your IOP to 3/93=1 to use point charges instead of s-Gaussians for nuclei, it is possible that analytic gradients might be available for that nuclear model. (2) If your system has symmetry, take advantage of it with a well constructed z-matrix and use opt=z-matrix as well. (3) change the default optimization method to something other than EF. The problem is that the deprecated Fletcher-Powell and Murtagh-Sargent methods also have this limitation. (4) consider the use of constrained geometries ie setting all C-H distances to be equal, optimize the rest. This can be done by partitioning your variables into 2 sets so that neither set is larger than 50 variables, and keep changing which set you optimize, until both sets of variables are converged. ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye^^^crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Tue Mar 13 22:07:00 2012 From: "Seth Olsen seth.olsen-x-uq.edu.au" To: CCL Subject: CCL: CASSCF does not produce spin densities Message-Id: <-46486-120313192634-16359-yqr0XePmZNqT5wUlt9Nefw^server.ccl.net> X-Original-From: Seth Olsen Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 14 Mar 2012 09:26:15 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [seth.olsen===uq.edu.au] With all due respect, I think this conversation is getting foolish. The concepts of "static" vs "dynamic" correlation do not have meaning in the context of CASSF models. That is, they usually don't have well-defined meaning in any case (I.e. everyone has their own) but any reasonable meaning falls apart in a complete active space context - because the space is complete! In the asymptotic limit where all orbitals are included, it becomes fill CI, and obviously treats both. I know of no sensible way to cleanly distinguish the turnover where "static" correlation ends and where "dynamic" correlation begins, regardless of the length of the expansion. This field needs a revision of its core concepts, soon. Slaughter this sacred cow before it rots on its own. Seth Olsen, Ph.D. ARC Australian Research Fellow School of Mathematics & Physics The University of Queensland Brisbane, QLD 4072 Australia +61 7 3365 2816 On 14/03/2012, at 4:17, "Neese, Frank frank.neese{:}mpi-mail.mpg.de" wrote: > In response to Georg and Jim: > > >> with all respect, but Frank Neese's statement is wrong. > > it looks like we are opening Pandora's box here :-) > > I nevertheless take the liberty to disagree with the statement brought forward by Georg. (Not with the stated facts of course. I do understand what CASSCF is and having programmed diverse multireference methods over the years I do claim to have at least some appreciation of multireference wavefunction theory; I know the Schlegl/Robb papers that were quoted by Georg; they report a convergence enhancement algorithm for CASSCF wave functions and an application to a reaction between two very small molecules, i.e. H2CO --> H2 + CO. Very nice work! But IMHO these papers do not disprove anything I said). > > My arguments in favor of stating what I have stated in my previous post are summarized below: > > As we all know CASSCF is limited to very few number of active orbitals. The majority of reseachers who have worked intensely in the field of multiconfigurational self consistent field theory agree that this type of wavefunction is not meant to cover dynamic correlation which is what would be required to really go beyond Hartree-Fock level accuracy. Compared to, say, a closed shell or ROHF CASSCF obviously does include a tiny amount of dynamic correlation (unless your active space is trivially small and reduces to the closed shell or ROHF determinant). However, that tiny little bit of dynamic correlation is essentially irrelevant. What CASSCF is designed to do is to generalize the Hartree-Fock method to cases where the single determinant Ansatz is qualitatively wrong. There are many papers by eminent researchers like Peter Pulay or Jean Paul Malrieu who state that it would be an abuse of the CASSCF method to want to cover more than the essential model space (which is the minimal active space that is needed to cover the static correlation; that again can mean many things. Sometimes it means ensuring that your dissociation limit is correctly represented. Obviously here is where ones chemical thinking comes in). I personally agree with this reasoning. It is then logical to state that CASSCF is not a high level method because its accuracy will be similar to that of, say, RHF in the cases where a closed shell determinant is reasonable. Thus, CASSCF is of broader applicability (even much broader) and it is more consistent than R(O)HF, but it is not of strikingly higher accuracy - provided one compares apples with apples and oranges with oranges. > > Of course if one defines anything that has more than one determinant as a post Hartree-Fock method then, yes, there is no doubt that CASSCF is post-HF. It is not, however, my favorite definition of what a post-HF method is designed to be. I would tend to use this term if it is implied that a substantial fraction of the (basis set) dynamic correlation energy is recovered by the treatment (what is meant by "dynamic correlation" is, again, a matter of the reference point. If you argue > from a multireference perturbation theory or multireference configuration interaction or multireference coupled cluster point of view then CASSCF is the starting point and does not contain dynamic correlation). > > At the end of the day everybody is of course free to do whatever calculation one wants and maybe one has good reasons for wanting to cover some dynamic correlation already with a CASSCF wave function. A typical example is the double d-shell effect for transition metal calculations in conjunction with the CASSCF/CASPT2 method that in particular Kristin Pierloot has elaborated on many times (in this case one covers a radial correlation effect). My personal preference, however, is to do this with a post-CASSCF treatment (if one can afford it). > > We too have had many good results with CASSCF and transition metals. My concerns were directed at the particular problem that the colleague was mentioning. Having worked on both, multireference wavefunctions and iron nitrosyl systems, I have simply expressed concerns to regard CASSCF as a high level treatment that should be given preference over any other theoretical method. To do so would, in my opinion, require solid backup > from comparison of calculated to observed physical properties. > > The discussion that we have been starting here could very quickly turn into a hair splitting dispute about terminology and I hope that this is not what will happen. I have simply tried here to explain what my take on the subject is and I do, of course, respect any other approach or opinion that leads to creative and interesting science. > > Best regards > Frank > > ------------------------------------------------------------------------- > Prof. Dr. Frank Neese > - Director - > Max-Planck Institut für Bioanorganische Chemie > Stiftstr. 34-36 > D-45470 Mülheim an der Ruhr > Germany > E-Mail: Frank.Neese]~[mpi-mail.mpg.de > ------------------------------------------------------------------------- >