From owner-chemistry@ccl.net Sun Feb 12 10:50:00 2006 From: "David Cornil cornildavid##yahoo.fr" To: CCL Subject: CCL: dipole_moment_with_AMPAC Message-Id: <-30856-060212095507-5240-T5kqwylpXFWd1vtNbbRIvg:_:server.ccl.net> X-Original-From: "David Cornil" Sent to CCL by: "David Cornil" [cornildavid---yahoo.fr] Dear CCLers, I make calculation about molecular stacks with an AMPAC package and I'm interested by the value of the dipole moment. In the file output there is the following lines : DIPOLE (Debye) X Y Z TOTAL POINT-CHG. HYBRID SUM When I calculate myself the dipole moment with the cartesian coordinates and the atomic charges (with the relation : ux = sum (X * Qx) ; uy = sum (Y * Qy ; uz = sum (Z * Qz) and finally u = sqr(ux^2 + uy^2 + uz^2)) I obtain the value of point-chg. My question is : What is the hydrid component and how is this component calculated ? Thanks for your help David Cornil From owner-chemistry@ccl.net Sun Feb 12 14:38:00 2006 From: "Ding Xunlei ding . sissa.it" To: CCL Subject: CCL:G: Lowdin and Mulliken population Message-Id: <-30857-060212113058-2816-tWkKV9LeHwkwgYMF7VGDSw::server.ccl.net> X-Original-From: Ding Xunlei Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sun, 12 Feb 2006 16:33:21 +0100 Mime-Version: 1.0 Sent to CCL by: Ding Xunlei [ding#sissa.it] Dear All, Using Gaussian03 with the input file below, we can get the Mulliken and Lowdin charge populations on CO2 molecule. But the results are totally opposite, as: Mulliken atomic charges: 1 C 1.006159 (lose electrons) 2 O -0.503080 3 O -0.503080 Lowdin Atomic Charges: 1 C -0.465607 (get electrons?) 2 O 0.232804 3 O 0.232804 Why? Thank you! Yours, Ding #pbepbe/6-311+G(3df) opt iop(6/80=1) mp2 0 1 C O 1 1.16 O 1 1.16 2 180.0 From owner-chemistry@ccl.net Sun Feb 12 20:56:00 2006 From: "Fuji Yama yamafuji6{=}yahoo.com" To: CCL Subject: CCL:G: ModRedundant in g03 Message-Id: <-30858-060212205442-11021-YYZYwnxo6fxpKDVP9okNcQ|*|server.ccl.net> X-Original-From: "Fuji Yama" Sent to CCL by: "Fuji Yama" [yamafuji6__yahoo.com] Dear CCL Members, I am trying to optimize the Trimer geometry of DNA Bases flanking with some ligands (Base-Ligand-Base) using some geometrical constrains (using Modredundant option and fixing some atoms between DNA bases and ligand). But modredundant option works only for molecular specification in Z-martix. So you please tell me 1) How to fix some bond length/angle between the base and ligand? 2) How to use Modredundant for XYZ coordinates? Please find the part of the Input and Log files below. Looking forward for your kind help. Thank you very much. Best Regards, Fuji. INPUT FILE ---------- %Chk=temp.chk %NProc=16 %Mem=16Gb B3LYP/6-311+G(d) test Opt(Modredundant) Pop=Regular gfprint SCRF=(CPCM, Solvent=Water) ground state geometry optimization (CPCM-Water, Room Temp) 1 1 H 6.02190 5.76490 33.11450 N 5.05460 5.48110 33.17780 C19 B C50 B ..... C19 C50 F ..... LOG FILE -------- The following ModRedundant input section has been read: Invalid extra data found. C19 B ? Error termination via Lnk1e in /usr/ap/g03/l101.exe at Sun Feb 12 20:23:43 2006. Job cpu time: 0 days 0 hours 0 minutes 1.5 seconds. File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 1 Scr= 1 ** Address Error ** From owner-chemistry@ccl.net Sun Feb 12 22:30:01 2006 From: "S.I.Gorelsky gorelsky[]stanford.edu" To: CCL Subject: CCL:G: Lowdin and Mulliken population Message-Id: <-30859-060212222803-5598-TvREznn3QXqVEkOlQKy07Q()server.ccl.net> X-Original-From: "S.I.Gorelsky" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 12 Feb 2006 19:27:52 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "S.I.Gorelsky" [gorelsky|-|stanford.edu] This is hardly surprising: you are using the 6-311+G(3df) basis set and MPA charges(populations) derived from calculations with diffuse(+) functions are bound to fail. For more details, you can check the AOMix manual, pages 7 and 57 (http://www.sg-chem.net/aomix). My recommendation: try to run your calculation with the TZVP basis set. Then both MPA and LPA should give you the reasonable numbers. Regards, S.G. On Sun, 12 Feb 2006, Ding Xunlei ding . sissa.it wrote: > Sent to CCL by: Ding Xunlei [ding#sissa.it] > Dear All, > > Using Gaussian03 with the input file below, we can get the Mulliken and > Lowdin charge populations on CO2 molecule. But the results are totally > opposite, as: > > Mulliken atomic charges: > 1 C 1.006159 (lose electrons) > 2 O -0.503080 > 3 O -0.503080 > Lowdin Atomic Charges: > 1 C -0.465607 (get electrons?) > 2 O 0.232804 > 3 O 0.232804 > > Why? > Thank you! > > Yours, > Ding > > #pbepbe/6-311+G(3df) opt iop(6/80=1) > > mp2 > > 0 1 > C > O 1 1.16 > O 1 1.16 2 180.0> > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From owner-chemistry@ccl.net Sun Feb 12 23:31:00 2006 From: "shayu li shalene_l%%yahoo.com" To: CCL Subject: CCL: computation of franck-condon factor Message-Id: <-30860-060212220304-2905-03mAG6gF/d1xZLt3CHWgYQ~~server.ccl.net> X-Original-From: "shayu li" Sent to CCL by: "shayu li" [shalene_l^_^yahoo.com] Who can give me some examples about ".LINEAR" in Dalton package? Thanks for your help Shayu Li