From owner-chemistry@ccl.net Wed Apr 21 00:52:01 2010 From: "Soren Eustis soreneustis],[gmail.com" To: CCL Subject: CCL:G: CCSD and MP2 Optimization error, but not for DFT?? Message-Id: <-41682-100421004706-24797-76LhEpaB9XqRzp7YFwl1Gw()server.ccl.net> X-Original-From: Soren Eustis Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes Date: Wed, 21 Apr 2010 06:47:30 +0200 Mime-Version: 1.0 (iPhone Mail 7E18) Sent to CCL by: Soren Eustis [soreneustis()gmail.com] Dear Jamin, I worked around this by using the opt(newton,nrscale) keywords. =20 Thanks for your response. Best, Soren On 19.04.2010, at 19:22, "Jamin Krinsky jamink()berkeley.edu" = wrote: > > Sent to CCL by: Jamin Krinsky [jamink]-[berkeley.edu] > Dear Soren, > I have been seeing this problem quite often since switching to G09. > I'm starting to think it comes from a bug in the new geometry > optimization algorithm (GEDIIS). I haven't tried this personally but > you might try using OPT=3DRFO to request the algorithm that was the > default in G03. > Regards, > Jamin > > On Fri, Apr 16, 2010 at 4:44 PM, Soren Eustis soreneustis ~~ gmail.com > wrote: >> Greetings, >> >> I am working on a simple system: M3O- (M=3DLi, K, Na, etc...). I =20= >> am able >> to get triplet and singlet ground states to converge fine with DFT, =20= >> but when >> I take those same geometries and submit them using MP2 or CCSD the =20= >> job >> always fails after several (sometimes more) iterations. The error =20= >> is that >> the coordinate system is inconsistent and =E2=80=98small interatomic = dista=20 >> nces=E2=80=99 were >> encountered. The geometry at the final iteration is not even =20 >> printed, and I >> see NaN (empty set) for some RMS values. >> >> This is really odd. I have tried my normal geometry opt tricks =20 >> (nrscale, >> maxstep), but no luck. This problem seems larger than that. Here =20= >> is the >> top and bottom of the output: >> >> %mem=3D8gb >> %nprocshared=3D8 >> Will use up to 8 processors via shared memory. >> %CHK=3Doutput.chk >> =20 >> ---=20 >> ------------------------------------------------------------------- >> #P CCSD/6-311++G(3d,3p) IOP(1/88=3D1) SCF(TIGHT,XQC) OPT=20 >> (TIGHT,maxcycle=3D >> 300) FREQ(noraman) NOSYMMETRY >> =20 >> ---=20 >> ------------------------------------------------------------------- >> >> >> >> ....... >> >> Berny optimization. >> Using GEDIIS/GDIIS optimizer. >> Internal Forces: Max 0.000930246 RMS 0.000664259 >> Search for a local minimum. >> Step number 3 out of a maximum of 100 >> All quantities printed in internal units (Hartrees-Bohrs-Radians) >> RMS Force =3D .66426D-03 SwitMx=3D.10000D-02 MixMth=3D 2 >> Mixed Optimization -- En-DIIS/RFO-DIIS >> Update second derivatives using D2CorX and points 1 2 3 >> DE=3D -7.87D-05 DEPred=3D-7.32D-05 R=3D 1.08D+00 >> SS=3D 1.41D+00 RLast=3D 3.79D-02 DXNew=3D 5.0454D-01 1.1371D-01 >> Trust test=3D 1.08D+00 RLast=3D 3.79D-02 DXMaxT set to 3.00D-01 >> The second derivative matrix: >> R1 R2 R3 R4 R5 >> R1 0.17194 >> R2 -0.02094 0.17194 >> R3 -0.02094 -0.02094 0.17194 >> R4 -0.00302 -0.00302 -0.00302 0.01693 >> R5 -0.00301 -0.00301 -0.00301 -0.00378 =20 >> 0.01694 >> R6 -0.00302 -0.00302 -0.00302 -0.00379 =20 >> -0.00378 >> R6 >> R6 0.01693 >> Use linear search instead of GDIIS. >> Eigenvalues --- 0.00869 0.02071 0.02072 0.13074 =20 >> 0.19288 >> Eigenvalues --- 0.19288 >> RFO step: Lambda=3D-2.29742560D-04 EMin=3D 8.68925581D-03 >> Quartic linear search produced a step of 1.43713. >> Iteration 1 RMS(Cart)=3D 0.34299183 RMS(Int)=3D 0.11881741 >> Iteration 2 RMS(Cart)=3D 0.23882000 RMS(Int)=3D 0.04698067 >> New curvilinear step failed, DQL=3D 3.65D-02 SP=3D-1.00D+00. >> Iteration 1 RMS(Cart)=3D 0.30937004 RMS(Int)=3D 0.10049878 >> Iteration 2 RMS(Cart)=3D 0.22088439 RMS(Int)=3D 0.04067145 >> New curvilinear step failed, DQL=3D 5.98D-02 SP=3D-1.00D+00. >> Iteration 1 RMS(Cart)=3D 0.27574815 RMS(Int)=3D 0.08414942 >> Iteration 2 RMS(Cart)=3D 0.20316690 RMS(Int)=3D 0.03476852 >> New curvilinear step failed, DQL=3D 9.13D-02 SP=3D-1.00D+00. >> Iteration 1 RMS(Cart)=3D 0.24212704 RMS(Int)=3D 0.06983656 >> Iteration 2 RMS(Cart)=3D 0.18566499 RMS(Int)=3D 0.02929391 >> New curvilinear step failed, DQL=3D 1.42D-01 SP=3D-1.00D+00. >> Iteration 1 RMS(Cart)=3D 0.20850556 RMS(Int)=3D 0.05761178 >> Iteration 2 RMS(Cart)=3D 0.16838286 RMS(Int)=3D 0.02426886 >> New curvilinear step failed, DQL=3D 2.49D-01 SP=3D-1.00D+00. >> Iteration 1 RMS(Cart)=3D 0.17488479 RMS(Int)=3D 0.04748671 >> Iteration 2 RMS(Cart)=3D 0.15102309 RMS(Int)=3D 0.01967343 >> New curvilinear step failed, DQL=3D 6.18D-01 SP=3D-1.00D+00. >> Iteration 1 RMS(Cart)=3D 0.14126403 RMS(Int)=3D 0.03938524 >> Iteration 2 RMS(Cart)=3D 0.12626319 RMS(Int)=3D 0.01457652 >> New curvilinear step failed, DQL=3D 1.38D+00 SP=3D-9.86D-01. >> Iteration 1 RMS(Cart)=3D 0.10764312 RMS(Int)=3D 0.03308054 >> Iteration 2 RMS(Cart)=3D 0.10610184 RMS(Int)=3D 0.01052722 >> New curvilinear step failed, DQL=3D 5.81D+00 SP=3D-9.46D-01. >> Iteration 1 RMS(Cart)=3D 0.07402396 RMS(Int)=3D 0.02815003 >> Iteration 2 RMS(Cart)=3D 0.08995262 RMS(Int)=3D 0.00743084 >> New curvilinear step failed, DQL=3D 9.82D-02 SP=3D-8.35D-01. >> Iteration 1 RMS(Cart)=3D 0.04040832 RMS(Int)=3D 0.02400387 >> Iteration 2 RMS(Cart)=3D 0.07796541 RMS(Int)=3D 0.00532937 >> Iteration 3 RMS(Cart)=3D 0.02900701 RMS(Int)=3D 0.00400663 >> New curvilinear step failed, DQL=3D 6.68D-02 SP=3D-8.06D-01. >> Iteration 1 RMS(Cart)=3D 3.42991671 RMS(Int)=3D 4.96605092 >> Iteration 2 RMS(Cart)=3D447.15764271 RMS(Int)=3D898.91069919 >> Iteration 3 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 4 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 5 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 6 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 7 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 8 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 9 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 10 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 11 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 12 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 13 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 14 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 15 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 16 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 17 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 18 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 19 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 20 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 21 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 22 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 23 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 24 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 25 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 26 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 27 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 28 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 29 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 30 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 31 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 32 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 33 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 34 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 35 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 36 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 37 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 38 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 39 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 40 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 41 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 42 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 43 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 44 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 45 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 46 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 47 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 48 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 49 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 50 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 51 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 52 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 53 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 54 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 55 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 56 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 57 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 58 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 59 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 60 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 61 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 62 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 63 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 64 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 65 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 66 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 67 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 68 RMS(Cart)=3D************ RMS(Int)=3D************ >> Iteration 69 RMS(Cart)=3D Inf RMS(Int)=3D Inf >> Iteration 70 RMS(Cart)=3D NaN RMS(Int)=3D NaN >> TrRot=3D 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 >> Variable Old X -DE/DX Delta X Delta X Delta X =20 >> New X >> (Linear) (Quad) (Total) >> R1 3.17933 0.00014 0.01492 -0.00622 NaN =20= >> NaN >> R2 3.17933 0.00014 0.01492 -0.00622 NaN =20= >> NaN >> R3 3.17934 0.00014 0.01492 -0.00622 NaN =20= >> NaN >> R4 5.50652 0.00093 0.02770 0.08074 NaN =20= >> NaN >> R5 5.50696 0.00093 0.02765 0.08060 NaN =20= >> NaN >> R6 5.50657 0.00093 0.02770 0.08072 NaN =20= >> NaN >> Item Value Threshold Converged? >> Maximum Force 0.000930 0.000015 NO >> RMS Force 0.000664 0.000010 NO >> Maximum Displacement NaN 0.000060 YES >> RMS Displacement NaN 0.000040 YES >> Predicted change in Energy=3D NaN >> =20 >> = GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad =20 >> >> Leave Link 103 at Fri Apr 16 13:40:38 2010, MaxMem=3D 1073741824 = cpu: >> 0.1 >> (Enter /home/soren/g09/l202.exe) >> Input orientation: >> =20 >> --------------------------------------------------------------------- >> Center Atomic Atomic Coordinates (Angstroms) >> Number Number Type X Y Z >> =20 >> --------------------------------------------------------------------- >> 1 8 0 NaN NaN =20= >> NaN >> 2 3 0 NaN NaN =20= >> NaN >> 3 3 0 NaN NaN =20= >> NaN >> 4 3 0 NaN NaN =20= >> NaN >> =20 >> --------------------------------------------------------------------- >> Distance matrix (angstroms): >> 1 2 3 4 >> 1 O 0.000000 >> 2 Li 0.000000 0.000000 >> 3 Li 0.000000 0.000000 0.000000 >> 4 Li 0.000000 0.000000 0.000000 0.000000 >> Small interatomic distances encountered: 2 1 3 =20 >> 1 3 >> 2 4 1 4 2 >> Small interatomic distances encountered: 4 3 >> Problem with the distance matrix. >> Error termination via Lnk1e in /home/soren/g09/l202.exe at Fri Apr =20= >> 16 >> 13:40:38 2010. >> Job cpu time: 0 days 6 hours 31 minutes 55.1 seconds. >> File lengths (MBytes): RWF=3D 3970 Int=3D 0 D2E=3D 0 =20= >> Chk=3D 2 >> Scr=3D 1 >> >> >> >> >> >> Thanks in advance! >> >> Soren >> >> >> -- >> Dr. Soren N. Eustis >> ETH =E2=80=93 Zurich >> Institute for Biogeochemistry and Pollutant Dynamics >> Universitatstrasse 16 >> 8092 Zurich >> >> +41 44 632 93 48 (office) >> +41 44 632 14 38 (fax) >> >> soren+*+env.ethz.ch >> >> > > > > --=20 > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink=3D=3D=3Dberkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > > > - This is automatically added to each message by the mailing script =3D-= > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> > From owner-chemistry@ccl.net Wed Apr 21 10:40:01 2010 From: "Lorenzo Ferro L.Ferro]*[sussex.ac.uk" To: CCL Subject: CCL:G: 4333111/433111/43 basis set calculation on Gaussian Message-Id: <-41683-100421090331-12609-CM+jN/Zc8FaWSvYSsaUUrg-x-server.ccl.net> X-Original-From: "Lorenzo Ferro" Date: Wed, 21 Apr 2010 09:03:30 -0400 Sent to CCL by: "Lorenzo Ferro" [L.Ferro ~~ sussex.ac.uk] The question might look silly, I am trying to run a single point energy calculation on Gaussian 03 using the [4333111/433111/43] basis set for the Sn atom, how do I have to set up the input file to use this basis set? Moreover, how do I add the polarization function for it? I thought that putting b3lyp/gen in the rout card and specifying Sn 0 4333111/433111/43 **** C H N O 6-31G* **** at the end would be ok, but apparently it is not... Thank you!!! Lorenzo ---------------------------- Lorenzo Ferro PhD Student University of Sussex BN1 9QJ Brighton UK email: L.Ferro[a]sussex.ac.uk ---------------------------- From owner-chemistry@ccl.net Wed Apr 21 15:09:00 2010 From: "Jamin Krinsky jamink,+,berkeley.edu" To: CCL Subject: CCL:G: 4333111/433111/43 basis set calculation on Gaussian Message-Id: <-41684-100421114555-20268-iZl89DEAgTRr054uam0rDA+*+server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Apr 2010 08:45:45 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink-$-berkeley.edu] Dear Lorenzo, The [4333111/433111/43] designation probably refers to a basis set contraction scheme (although the format looks odd), not an actual basis set name. Did you see this in an article (maybe just that and the name of the group that made it)? You need to either enter a Gaussian-recognized BS name or the basis set itself (w/ coefficients and exponents). Many basis sets can be found at the EMSL site (https://bse.pnl.gov/bse/portal). For directions on how to enter a general basis, you might take a look at our facility web page where I put together some common format types. The link is: http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html Also, it looks like you omitted the 0 (zero) at the end of the C H N O specification, which will result in an error. Assuming that's oxygen in your specs, that line should read C H N O 0. Regards, Jamin On Wed, Apr 21, 2010 at 6:03 AM, Lorenzo Ferro L.Ferro]*[sussex.ac.uk wrote: > > Sent to CCL by: "Lorenzo =A0Ferro" [L.Ferro ~~ sussex.ac.uk] > The question might look silly, I am trying to run a single point energy c= alculation on Gaussian 03 using the [4333111/433111/43] basis set for the S= n atom, how do I have to set up the input file to use this basis set? Moreo= ver, how do I add the polarization function for it? > > I thought that putting b3lyp/gen in the rout card and specifying > > Sn 0 > 4333111/433111/43 > **** > C H N O > 6-31G* > **** > > at the end would be ok, but apparently it is not... > > Thank you!!! > > Lorenzo > > > ---------------------------- > Lorenzo Ferro > PhD Student > University of Sussex > BN1 9QJ Brighton UK > email: L.Ferro[*]sussex.ac.uk > ---------------------------- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink|,|berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Wed Apr 21 18:20:00 2010 From: "Lorenzo Ferro L.Ferro**sussex.ac.uk" To: CCL Subject: CCL:G: 4333111/433111/43 basis set calculation on Gaussian Message-Id: <-41685-100421180654-31152-ImJI+MLUsLk8Ad/+oL+cbA^^^server.ccl.net> X-Original-From: "Lorenzo Ferro" Date: Wed, 21 Apr 2010 18:06:52 -0400 Sent to CCL by: "Lorenzo Ferro" [L.Ferro(0)sussex.ac.uk] Hi Jamin, thanks for the reply and for the link on custom basis set as it answered some doubts that I had! Here is the article where I saw it (pubs.acs.org/doi/abs/10.1021/ja9068408), but it is not the only one, I found a few more. Following the experimental section of the mentioned article how should the input file be then? (btw, I omitted the zero only here not in the calculation) Thanks for your help!!! Lorenzo > "Jamin Krinsky jamink,+,berkeley.edu" wrote: > > Sent to CCL by: Jamin Krinsky [jamink-$-berkeley.edu] > Dear Lorenzo, > > The [4333111/433111/43] designation probably refers to a basis set > contraction scheme (although the format looks odd), not an actual > basis set name. Did you see this in an article (maybe just that and > the name of the group that made it)? You need to either enter a > Gaussian-recognized BS name or the basis set itself (w/ coefficients > and exponents). Many basis sets can be found at the EMSL site > (https://bse.pnl.gov/bse/portal). For directions on how to enter a > general basis, you might take a look at our facility web page where I > put together some common format types. The link is: > http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html > > Also, it looks like you omitted the 0 (zero) at the end of the C H N O > specification, which will result in an error. Assuming that's oxygen > in your specs, that line should read C H N O 0. > > Regards, > Jamin > > > On Wed, Apr 21, 2010 at 6:03 AM, Lorenzo Ferro L.Ferro]*[sussex.ac.uk > wrote: > > > > Sent to CCL by: "Lorenzo =A0Ferro" [L.Ferro ~~ sussex.ac.uk] > > The question might look silly, I am trying to run a single point energy c= > alculation on Gaussian 03 using the [4333111/433111/43] basis set for the S= > n atom, how do I have to set up the input file to use this basis set? Moreo= > ver, how do I add the polarization function for it? > > > > I thought that putting b3lyp/gen in the rout card and specifying > > > > Sn 0 > > 4333111/433111/43 > > **** > > C H N O > > 6-31G* > > **** > > > > at the end would be ok, but apparently it is not... > > > > Thank you!!! > > > > Lorenzo > > > > > > ---------------------------- > > Lorenzo Ferro > > PhD Student > > University of Sussex > > BN1 9QJ Brighton UK > > email: L.Ferro[*]sussex.ac.uk > > ---------------------------- > > > > > > > > -=3D This is automatically added to each message by the mailing script = > =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > > > > > > > --=20 > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink|,|berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > From owner-chemistry@ccl.net Wed Apr 21 22:45:00 2010 From: "Jamin Krinsky jamink**berkeley.edu" To: CCL Subject: CCL:G: 4333111/433111/43 basis set calculation on Gaussian Message-Id: <-41686-100421202808-23915-/zmOHwQPTyeaRAKpxtYi7A#%#server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Apr 2010 17:27:58 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink|-|berkeley.edu] The article you cited doesn't state what the basis set is named, but they did cite a book by Huzinaga which presumably contains the data. FYI what's now termed MIDI is also a Huzinaga basis but I think the one you're after is larger than that. You can try doing a Science Citation Search on that book and see if anyone referencing it cared to tabulate the basis set. Someone else on this forum might be able to tell you where to look more easily. Jamin On Wed, Apr 21, 2010 at 3:06 PM, Lorenzo Ferro L.Ferro**sussex.ac.uk wrote: > > Sent to CCL by: "Lorenzo =A0Ferro" [L.Ferro(0)sussex.ac.uk] > Hi Jamin, > > thanks for the reply and for the link on custom basis set as it answered = some doubts that I had! > Here is the article where I saw it (pubs.acs.org/doi/abs/10.1021/ja906840= 8), but it is not the only one, I found a few more. Following the experimen= tal section of the mentioned article how should the input file be then? > > (btw, I omitted the zero only here not in the calculation) > > Thanks for your help!!! > > Lorenzo > > >> "Jamin Krinsky jamink,+,berkeley.edu" =A0wrote: >> >> Sent to CCL by: Jamin Krinsky [jamink-$-berkeley.edu] >> Dear Lorenzo, >> >> The [4333111/433111/43] designation probably refers to a basis set >> contraction scheme (although the format looks odd), not an actual >> basis set name. Did you see this in an article (maybe just that and >> the name of the group that made it)? You need to either enter a >> Gaussian-recognized BS name or the basis set itself (w/ coefficients >> and exponents). Many basis sets can be found at the EMSL site >> (https://bse.pnl.gov/bse/portal). For directions on how to enter a >> general basis, you might take a look at our facility web page where I >> put together some common format types. The link is: >> http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html >> >> Also, it looks like you omitted the 0 (zero) at the end of the C H N O >> specification, which will result in an error. Assuming that's oxygen >> in your specs, that line should read C H N O 0. >> >> Regards, >> Jamin >> >> >> On Wed, Apr 21, 2010 at 6:03 AM, Lorenzo Ferro L.Ferro]*[sussex.ac.uk >> wrote: >> > >> > Sent to CCL by: "Lorenzo =3DA0Ferro" [L.Ferro ~~ sussex.ac.uk] >> > The question might look silly, I am trying to run a single point energ= y c=3D >> alculation on Gaussian 03 using the [4333111/433111/43] basis set for th= e S=3D >> n atom, how do I have to set up the input file to use this basis set? Mo= reo=3D >> ver, how do I add the polarization function for it? >> > >> > I thought that putting b3lyp/gen in the rout card and specifying >> > >> > Sn 0 >> > 4333111/433111/43 >> > **** >> > C H N O >> > 6-31G* >> > **** >> > >> > at the end would be ok, but apparently it is not... >> > >> > Thank you!!! >> > >> > Lorenzo >> > >> > >> > ---------------------------- >> > Lorenzo Ferro >> > PhD Student >> > University of Sussex >> > BN1 9QJ Brighton UK >> > email: L.Ferro[*]sussex.ac.uk >> > ---------------------------- >> > >> > >> > >> > -=3D3D This is automatically added to each message by the mailing scri= pt =3D >> =3D3D-> =3DA0 =3DA0 =3DA0http://www.ccl.net/cgi-bin/ccl/send_ccl_message= > =3DA0 =3DA0 =3DA0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =3DA0 = =3DA0 =3DA0http://www.ccl.net/chemistry/sub_unsub.shtml> =3DA0 =3DA0 =3DA0h= ttp://www.ccl.net/spammers.txt> >> > >> > >> >> >> >> --=3D20 >> Jamin L Krinsky, Ph.D. >> Molecular Graphics and Computation Facility >> 175 Tan Hall, University of California, Berkeley, CA 94720 >> jamink|,|berkeley.edu, 510-643-0616 >> http://glab.cchem.berkeley.edu >> >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink|-|berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Wed Apr 21 23:20:00 2010 From: "Kalju Kahn kalju,chem.ucsb.edu" To: CCL Subject: CCL: Rate constant Message-Id: <-41687-100421212144-16278-evSruPNsywUXhpMfYYkt0w ~ server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 21 Apr 2010 17:42:16 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju++chem.ucsb.edu] Hi Lydia, I am posting a few ideas regarding TST in solution but I do not pretend that I know what is a correct way of doing what you are hoping to do. Instead, I hope that someone with a better knowledge of the topic will extend this thread ... it is definitely an interesting topic. 1) The partition functions are calculated based on ideal gas (Qt), rigid rotor (Qr), and harmonic oscillator (Qv) models. Optimizing the geometry with polarizable solvent, and redoing vibrational analysis is not going to give you the partition functions of the dissolved molecule ... Qt formula is still for the particle-in-the box/ideal gas case. It is not entirely clear how one should deal with Qt or Qr in the solution (what is the free volume for solute translation? Is the rotation of the solute in the solvent as free as in the gas phase?). 2) Implicit solvation calculations give usually some sort of "free energy" for the solute. But SCRF or PCM give "free energies" without doing an explicit vibrational analysis! This is so because some terms in these methods have been parametrized to reproduce experimental free energies. This has two implications. First, it seems wrong to add explicit vibrational corrections to SCRF "free energies". Second, one can only guess how well the parametrized model deals with transition states that have rather unusual electron distributions. 3) The standard state in the gas phase (1 atm) and solution (1M) are different; a correction of 1.89 kcal/mol may be needed depending on the molarity of the process. 4) Non-equilibrium solvation / recrossing might be important in the solvent. I seem to recall that these effects may alter the magnitude of k by factor of 10 or less. This was studied by Kramers as early as in 1940s. More recently, Warshel's group has addressed these issues rather thoroughly. However, many authors ignore the possibility of recrossing when discussing their ab initio solution phase rate constants based on TST. 5) Tunneling appears to be affected by solvent friction and/or solvent dynamics. A good amount of work has been done on electron transfer. A rather old review by Hynes (Ann. Rev. Phys. Chem 1985, 36, 573) still makes useful reading about this topic. Hope this helps, Kalju > > Sent to CCL by: "Lydia Rhyman" [lydrhy**hotmail.com] > Dear CClers, > > Greetings > > I have used the conventional transition state theory to calculate the rate > constant of a reaction with the Wigner tunneling coefficient ( ) in the > gas > phase using the equation below: > > k=(KbT/h)(QtsNa/Q1Q2)exp(-Ea/RT) > > 1, 2 and TS have been fully optimised in the gas phase and Qs have been > calculated from frequencies. > > I want to extend to solvent phase. > Can the same procedure be used? > Does the rate equation change? > > I will appreciate your response/hint. > Kind regards > > Lydia Rhyman> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106