From owner-chemistry@ccl.net Thu Oct 15 02:23:00 2009 From: "Abhishek DuttaChowdhury abhishekdc~~chem.iitb.ac.in" To: CCL Subject: CCL: g03 error Message-Id: <-40470-091015021414-22526-uLwSx55in7VRJyj0eg7BSA#,#server.ccl.net> X-Original-From: "Abhishek DuttaChowdhury" Date: Thu, 15 Oct 2009 02:14:10 -0400 Sent to CCL by: "Abhishek DuttaChowdhury" [abhishekdc,,chem.iitb.ac.in] Dear All, I am doing one transition state optimization but mu job stucks at after 1st step. Job is running but output file is not updated and/or expanding according to that. My input file: %chk=TS2.chk %mem=500MB #B3LYP/gen opt=(TS,CalcFc,NoEigen) Nosymm Pseudo=Read formcheck GFINPUT IOp(6/7=3) #P GFPRINT 0 1 ... ... coordinates ... .. At the end of my output file: EnCoef did 100 forward-backward iterations SCF Done: E(RB+HF-LYP) = -1976.84529817 A.U. after 18 cycles Convg = 0.4826D-08 -V/T = 2.0560 S**2 = 0.0000 Range of M.O.s used for correlation: 1 770 NBasis= 770 NAE= 176 NBE= 176 NFC= 0 NFV= 0 NROrb= 770 NOA= 176 NOB= 176 NVA= 594 NVB= 594 1 Symmetry operations used in ECPInt. ECPInt: NShTT= 40470 NPrTT= 247723 LenC2= 28493 LenP2D= 85711. LDataN: DoStor=F MaxTD1= 6 Len= 172 LDataN: DoStor=T MaxTD1= 6 Len= 172 ECPInt: NShTT= 40470 NPrTT= 247723 LenC2= 28493 LenP2D= 85711. LDataN: DoStor=F MaxTD1= 6 Len= 172 LDataN: DoStor=T MaxTD1= 6 Len= 172 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 23 centers at a time, making 4 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0. Defaulting to unpruned grid for atomic number 46. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0. What is the meaning of last line? Does anyone know why it's stuck here? Is there some way I can check where I'm getting stuck? What are the possible solution? Thanks in advance Sincerely, Abhishek From owner-chemistry@ccl.net Thu Oct 15 10:15:01 2009 From: "Sharan sara180681#%#gmail.com" To: CCL Subject: CCL: Launching Green Chemistry Portal, a Free Green Chemistry reaction database Message-Id: <-40471-091015101335-4615-E/2kdxRdWHyZwKi/UaeVRg^_^server.ccl.net> X-Original-From: Sharan Content-Type: multipart/alternative; boundary=001636c59534e11cd20475f9e1bf Date: Thu, 15 Oct 2009 19:43:23 +0530 MIME-Version: 1.0 Sent to CCL by: Sharan [sara180681,,gmail.com] --001636c59534e11cd20475f9e1bf Content-Type: text/plain; charset=ISO-8859-1 Dear All We have launched a new portal named *GreenerChem.org a beta version. *This portal is targeted towards Organic chemist who would be interested in looking information on green reactions. Please Click Here: *Green Chemistry Portal* 1) Please Register for browsing the portal it take few minutes. 2) Please use IE (Internet Explorer ) as browser. 3) I would appreciate your suggestions and feedback to make this portal better. *Note:* *We also have plans to make this project an open source development, in this context i am sending this link for all the computational chemist. If you are interested, please Visit contact us* section of the portal *and write to us using relevant email contact.* With regards. SARAVANAN.I Jr. Scientist Chemoinformatics http://www.linkedin.com/in/saravananilangovan --001636c59534e11cd20475f9e1bf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear = All
We have launched a new portal named= =A0 GreenerChem.org a beta version. = This portal is targeted towards=A0Organic chemist who would be inter= ested in looking information on green reactions.
Please Click Here: Green Chemistry Portal
1) Please Register for browsing the = portal it take few minutes.=A0
2) Please use IE (Internet Explorer= =A0) as browser.=A0
3) I would appreciate your suggestio= ns and feedback to make this portal better.
Note: We also have plans to mak= e this project an open source development, in this context i am sending thi= s link for all the computational chemist. If you are interested, please Vis= it contact us section of the portal and write to us using relevant email contact.
With regards.
SARAVANAN.I
Jr.= Scientist Chemoinformatics

http://www.linkedin.com/in/saravananila= ngovan
--001636c59534e11cd20475f9e1bf-- From owner-chemistry@ccl.net Thu Oct 15 10:50:01 2009 From: "Alexander Hoepker achoepker,gmail.com" To: CCL Subject: CCL: B2PLYP-D Message-Id: <-40472-091015102209-8546-EyKEL0Uy92B9fDZaKfwoew[#]server.ccl.net> X-Original-From: Alexander Hoepker Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 15 Oct 2009 10:21:58 -0400 MIME-Version: 1.0 Sent to CCL by: Alexander Hoepker [achoepker:_:gmail.com] I have been using B3LYP with a 6-31G(d) basis set in the past but am now considering to switch over to the double hybrid DFT functional B2PLYP, perhaps with a dispersion correction (B2PLYP-D). I am working on 1st row only organic molecules with up to 35 non-hydrogen atoms. Grimme notes that B2PLYP should be used with a good polarization basis set such as TZVP or even QZVP. This strikes me as very expensive for a geometry optimization; but perhaps a simple Pople basis set would be sufficient for a geometry optimization and a more elaborate basis set could then be used for the frequency calculation. In other words. This leads me to two questions: (1) Do I forfeit the accuracy of B2PLYP with a basis set such as 6-31G(d)? (2) Is there a big advantage of B2PLYP over B3LYP with respect to geometry. (3) Is B2PLYP (or B2PLYP-D) computationally more demanding than B3LYP with the same basis set? I apologize if these questions are rather mondane but as an organic chemist the field of computational chemistry is often bewildering. With best regards, Alex From owner-chemistry@ccl.net Thu Oct 15 13:15:00 2009 From: "Sten Nilsson Lill stenil- -chem.gu.se" To: CCL Subject: CCL:G: B2PLYP-D Message-Id: <-40473-091015130240-32722-8oeRABVyR67Lym2/yE0SqA a server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 15 Oct 2009 18:24:25 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil##chem.gu.se] Dear Alexander, an alternative and cheaper solution could be to use DiLabio's B3LYP-DCP method, which has a dispersion correction potential added on top of standard B3LYP, see http://pubs.acs.org/doi/abs/10.1021/jp806162t . The recommendation is to use the 6-31+G(d,p) basis set. I did some benchmark tests on B3LYP-DCP recently, you can find the paper here: http://pubs.acs.org/doi/abs/10.1021/jp903995e There you will also find references to the papers by DiLabio with the background and development of the dispersion correction. Also, you will find a description on how to perform the calculations using for example Gaussian. Please note that different functionals and different basis sets have different dispersion correction potentials so if you try different combinations you just need to be a bit careful. The nice thing with B3LYP-DCP is that you can compare your results with standard B3LYP and directly evaluate the effects from the dispersion correction potential, both in terms of geometry and energies. Hope that helps, Sten > > Sent to CCL by: Alexander Hoepker [achoepker:_:gmail.com] > I have been using B3LYP with a 6-31G(d) basis set in the past but am > now considering to switch over to the double hybrid DFT functional > B2PLYP, perhaps with a dispersion correction (B2PLYP-D). I am working > on 1st row only organic molecules with up to 35 non-hydrogen atoms. > > Grimme notes that B2PLYP should be used with a good polarization basis > set such as TZVP or even QZVP. This strikes me as very expensive for a > geometry optimization; but perhaps a simple Pople basis set would be > sufficient for a geometry optimization and a more elaborate basis set > could then be used for the frequency calculation. In other words. This > leads me to two questions: > > (1) Do I forfeit the accuracy of B2PLYP with a basis set such as 6-31G(d)? > (2) Is there a big advantage of B2PLYP over B3LYP with respect to > geometry. > (3) Is B2PLYP (or B2PLYP-D) computationally more demanding than B3LYP > with the same basis set? > > I apologize if these questions are rather mondane but as an organic > chemist the field of computational chemistry is often bewildering. > > With best regards, > Alex> > > Ph. D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg Kemigården 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2873 Fax: +46-31-772 3840 E-mail: stenil*chem.gu.se Alternative e-mail: stenil*physto.se