From owner-chemistry@ccl.net Wed Feb 26 10:14:01 2014 From: "Shahar Keinan skeinan*gmail.com" To: CCL Subject: CCL: Gamess + Tinker QM/MM Message-Id: <-49809-140226101309-6135-cAxdac+z2cmC44+ppphDfg+/-server.ccl.net> X-Original-From: "Shahar Keinan" Date: Wed, 26 Feb 2014 10:13:08 -0500 Sent to CCL by: "Shahar Keinan" [skeinan^gmail.com] Good morning, I am looking for an open source QM/MM code, that is also parallel and free for commercial users. We are interested in using this on biological systems: ~100Ks MM atoms, ~100 QM atoms. Has anybody have experience with the Gamess/Tinker QM/MM combo? Can you share your experience? How easy was it to install and to run? How easy to produce the input files from PDBs? Are there good tools for run analysis? Thank you for your insight, Best, Shahar From owner-chemistry@ccl.net Wed Feb 26 10:59:00 2014 From: "Bedamani Singh bedamani11^gmail.com" To: CCL Subject: CCL:G: How to determine specific orbital in TDDFT calculation Message-Id: <-49810-140226101224-5953-augKbjXCFJhTQ+v9Myo+Jw*_*server.ccl.net> X-Original-From: "Bedamani Singh" Date: Wed, 26 Feb 2014 10:12:23 -0500 Sent to CCL by: "Bedamani Singh" [bedamani11!=!gmail.com] I have done tddft calculation for Pt2 cluster using gaussian 09. For the first excited state, the orbitals and corresponding coefficients of wavefunctions appears as given below. I need to determine the specific type of orbital transformation for this excited state. For this purpose, whether should I take the first entry (i.e. 15A -> 20A) or the one with largest coeffiecient i.e. 17B -> 19B ? To be more specific, I want to determine (i) the specific orbitals (i.e. s, or px,..., or dxy, or dyz,... orbitals) involved in this transition from the initial to excited states and also (ii)For all these transitions, I squared each coefficent and multiplied by 2 (for two spins), then follwed by 100(for percentage). Then sum up all these values which gives me 230.8249. But I think this value should be 100 as these are the sum of the percentage contribution to the transition. How I can interprete this result? (iii)the symmetry of the excited state. I am unable to find any specific information about these from the gaussian output fles. Please help me and any kind of suggestion will be higly appreciated. ******************************************************************************* Initial Symmetry: SGG Excitation energies and oscillator strengths: Excited state symmetry could not be determined. Excited State1:3.010-?Sym 0.1564eV 7928.53nm f=0.0001 =2.014 15A -> 20A 0.01970 18A -> 22A 0.01115 9B -> 22B 0.01670 9B -> 29B 0.01092 9B -> 36B -0.01291 14B -> 22B -0.01909 14B -> 29B -0.01112 14B -> 36B 0.01188 15B -> 18B -0.23779 16B -> 19B 0.23801 17B -> 19B 0.97991 17B -> 25B -0.03730 17B -> 31B 0.01473 17B -> 41B -0.01352 15A <- 20A 0.01702 18A <- 22A 0.01053 11B <- 27B -0.01098 11B <- 37B -0.01606 15B <- 18B -0.03051 16B <- 19B 0.03059 17B <- 19B 0.27278 17B <- 25B -0.01248 ************************************************************************** The detail information about the population analysis and alpha and beta Molecular Orbital Coefficients are also given Population analysis using the SCF density. Orbital symmetries: Alpha Orbitals: Occupied (SGG) (SGU) (SGG) (SGU) (PIU) (PIU) (PIG) (PIG) (SGG) (PIU) (PIU) (DLTG) (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGG) (SGU) Virtual (SGU) (PIU) (PIU) (SGG) (PIG) (PIG) (SGU) (SGG) (PIU) (PIU) (PIG) (PIG) (SGU) (DLTG) (DLTG) (PIU) (PIU) (SGG) (DLTU) (DLTU) (PIG) (PIG) (SGU) (SGG) (SGU) Beta Orbitals: Occupied (SGG) (SGU) (SGG) (SGU) (PIU) (PIU) (PIG) (PIG) (SGG) (PIU) (PIU) (DLTG) (DLTG) (SGG) (DLTU) (DLTU) (SGU) Virtual (PIG) (PIG) (SGU) (PIU) (PIU) (SGG) (PIG) (PIG) (SGU) (SGG) (PIU) (PIU) (PIG) (PIG) (SGU) (DLTG) (DLTG) (PIU) (PIU) (SGG) (DLTU) (DLTU) (PIG) (PIG) (SGU) (SGG) (SGU) The electronic state is 3-SGG. ********************************************************************************** Alpha Molecular Orbital Coefficients: 11 12 13 14 15 (PIU)--O (DLTG)-- (DLTG)-- (PIG)--O (PIG)--O Eigenvalues -- -0.35784 -0.28240 -0.28240 -0.27250 -0.27250 1 1 Pt 1S 0.00000 0.00000 0.00000 0.00000 0.00000 2 2S 0.00000 0.00000 0.00000 0.00000 0.00000 3 3S 0.00000 0.00000 0.00000 0.00000 0.00000 4 4PX 0.00000 0.00000 0.00000 -0.03551 0.00000 5 4PY 0.02178 0.00000 0.00000 0.00000 -0.03551 6 4PZ 0.00000 0.00000 0.00000 0.00000 0.00000 7 5PX 0.00000 0.00000 0.00000 0.04122 0.00000 8 5PY -0.01044 0.00000 0.00000 0.00000 0.04122 9 5PZ 0.00000 0.00000 0.00000 0.00000 0.00000 10 6PX 0.00000 0.00000 0.00000 0.01148 0.00000 11 6PY 0.00141 0.00000 0.00000 0.00000 0.01148 12 6PZ 0.00000 0.00000 0.00000 0.00000 0.00000 13 7D 0 0.00000 0.00000 0.00000 0.00000 0.00000 14 7D+1 0.00000 0.00000 0.00000 0.65955 0.00000 15 7D-1 0.60995 0.00000 0.00000 0.00000 0.65955 16 7D+2 0.00000 0.00000 0.62003 0.00000 0.00000 17 7D-2 0.00000 0.62003 0.00000 0.00000 0.00000 18 8D 0 0.00000 0.00000 0.00000 0.00000 0.00000 19 8D+1 0.00000 0.00000 0.00000 0.16341 0.00000 20 8D-1 0.12702 0.00000 0.00000 0.00000 0.16341 21 8D+2 0.00000 0.00000 0.14962 0.00000 0.00000 22 8D-2 0.00000 0.14962 0.00000 0.00000 0.00000 23 2 Pt 1S 0.00000 0.00000 0.00000 0.00000 0.00000 24 2S 0.00000 0.00000 0.00000 0.00000 0.00000 25 3S 0.00000 0.00000 0.00000 0.00000 0.00000 26 4PX 0.00000 0.00000 0.00000 0.03551 0.00000 27 4PY 0.02178 0.00000 0.00000 0.00000 0.03551 28 4PZ 0.00000 0.00000 0.00000 0.00000 0.00000 29 5PX 0.00000 0.00000 0.00000 -0.04122 0.00000 30 5PY -0.01044 0.00000 0.00000 0.00000 -0.04122 31 5PZ 0.00000 0.00000 0.00000 0.00000 0.00000 32 6PX 0.00000 0.00000 0.00000 -0.01148 0.00000 33 6PY 0.00141 0.00000 0.00000 0.00000 -0.01148 34 6PZ 0.00000 0.00000 0.00000 0.00000 0.00000 35 7D 0 0.00000 0.00000 0.00000 0.00000 0.00000 36 7D+1 0.00000 0.00000 0.00000 0.65955 0.00000 37 7D-1 -0.60995 0.00000 0.00000 0.00000 0.65955 38 7D+2 0.00000 0.00000 0.62003 0.00000 0.00000 39 7D-2 0.00000 0.62003 0.00000 0.00000 0.00000 40 8D 0 0.00000 0.00000 0.00000 0.00000 0.00000 41 8D+1 0.00000 0.00000 0.00000 0.16341 0.00000 42 8D-1 -0.12702 0.00000 0.00000 0.00000 0.16341 43 8D+2 0.00000 0.00000 0.14962 0.00000 0.00000 44 8D-2 0.00000 0.14962 0.00000 0.00000 0.00000 16 17 18 19 20 (DLTU)-- (DLTU)-- (SGG)--O (SGU)--O (SGU)--V Eigenvalues -- -0.26241 -0.26241 -0.26145 -0.25360 -0.14302 1 1 Pt 1S 0.00000 0.00000 0.20156 -0.06959 0.19375 2 2S 0.00000 0.00000 -0.26516 0.09635 -0.24891 3 3S 0.00000 0.00000 0.42593 0.00899 0.67653 4 4PX 0.00000 0.00000 0.00000 0.00000 0.00000 5 4PY 0.00000 0.00000 0.00000 0.00000 0.00000 6 4PZ 0.00000 0.00000 0.03283 -0.05315 -0.09761 7 5PX 0.00000 0.00000 0.00000 0.00000 0.00000 8 5PY 0.00000 0.00000 0.00000 0.00000 0.00000 9 5PZ 0.00000 0.00000 -0.02628 -0.08204 0.21543 10 6PX 0.00000 0.00000 0.00000 0.00000 0.00000 11 6PY 0.00000 0.00000 0.00000 0.00000 0.00000 12 6PZ 0.00000 0.00000 0.00418 -0.00931 0.01688 13 7D 0 0.00000 0.00000 -0.26724 0.62694 0.14982 14 7D+1 0.00000 0.00000 0.00000 0.00000 0.00000 15 7D-1 0.00000 0.00000 0.00000 0.00000 0.00000 16 7D+2 0.00000 0.64186 0.00000 0.00000 0.00000 17 7D-2 0.64187 0.00000 0.00000 0.00000 0.00000 18 8D 0 0.00000 0.00000 -0.02648 0.20033 0.06553 19 8D+1 0.00000 0.00000 0.00000 0.00000 0.00000 20 8D-1 0.00000 0.00000 0.00000 0.00000 0.00000 21 8D+2 0.00000 0.15349 0.00000 0.00000 0.00000 22 8D-2 0.15348 0.00000 0.00000 0.00000 0.00000 23 2 Pt 1S 0.00000 0.00000 0.20156 0.06959 -0.19375 24 2S 0.00000 0.00000 -0.26516 -0.09635 0.24891 25 3S 0.00000 0.00000 0.42593 -0.00899 -0.67653 26 4PX 0.00000 0.00000 0.00000 0.00000 0.00000 27 4PY 0.00000 0.00000 0.00000 0.00000 0.00000 28 4PZ 0.00000 0.00000 -0.03283 -0.05315 -0.09761 29 5PX 0.00000 0.00000 0.00000 0.00000 0.00000 30 5PY 0.00000 0.00000 0.00000 0.00000 0.00000 31 5PZ 0.00000 0.00000 0.02628 -0.08204 0.21543 32 6PX 0.00000 0.00000 0.00000 0.00000 0.00000 33 6PY 0.00000 0.00000 0.00000 0.00000 0.00000 34 6PZ 0.00000 0.00000 -0.00418 -0.00931 0.01688 35 7D 0 0.00000 0.00000 -0.26724 -0.62694 -0.14982 36 7D+1 0.00000 0.00000 0.00000 0.00000 0.00000 37 7D-1 0.00000 0.00000 0.00000 0.00000 0.00000 38 7D+2 0.00000 -0.64186 0.00000 0.00000 0.00000 39 7D-2 -0.64187 0.00000 0.00000 0.00000 0.00000 40 8D 0 0.00000 0.00000 -0.02648 -0.20033 -0.06553 41 8D+1 0.00000 0.00000 0.00000 0.00000 0.00000 42 8D-1 0.00000 0.00000 0.00000 0.00000 0.00000 43 8D+2 0.00000 -0.15349 0.00000 0.00000 0.00000 44 8D-2 -0.15348 0.00000 0.00000 0.00000 0.00000 ***************************************************************************** Beta Molecular Orbital Coefficients: 16 17 18 19 20 (DLTU)-- (SGU)--O (PIG)--V (PIG)--V (SGU)--V Eigenvalues -- -0.24473 -0.24124 -0.15774 -0.15774 -0.12861 1 1 Pt 1S 0.00000 -0.08639 0.00000 0.00000 0.18157 2 2S 0.00000 0.11837 0.00000 0.00000 -0.23525 3 3S 0.00000 -0.05644 0.00000 0.00000 0.65178 4 4PX 0.00000 0.00000 -0.04421 0.00000 0.00000 5 4PY 0.00000 0.00000 0.00000 -0.04421 0.00000 6 4PZ 0.00000 -0.04735 0.00000 0.00000 -0.10025 7 5PX 0.00000 0.00000 0.05274 0.00000 0.00000 8 5PY 0.00000 0.00000 0.00000 0.05274 0.00000 9 5PZ 0.00000 -0.08808 0.00000 0.00000 0.19553 10 6PX 0.00000 0.00000 0.05072 0.00000 0.00000 11 6PY 0.00000 0.00000 0.00000 0.05072 0.00000 12 6PZ 0.00000 -0.00310 0.00000 0.00000 0.04830 13 7D 0 0.00000 0.60831 0.00000 0.00000 0.19122 14 7D+1 0.00000 0.00000 0.63699 0.00000 0.00000 15 7D-1 0.00000 0.00000 0.00000 0.63699 0.00000 16 7D+2 0.63722 0.00000 0.00000 0.00000 0.00000 17 7D-2 0.00000 0.00000 0.00000 0.00000 0.00000 18 8D 0 0.00000 0.20089 0.00000 0.00000 0.08222 19 8D+1 0.00000 0.00000 0.20061 0.00000 0.00000 20 8D-1 0.00000 0.00000 0.00000 0.20061 0.00000 21 8D+2 0.16263 0.00000 0.00000 0.00000 0.00000 22 8D-2 0.00000 0.00000 0.00000 0.00000 0.00000 23 2 Pt 1S 0.00000 0.08639 0.00000 0.00000 -0.18157 24 2S 0.00000 -0.11837 0.00000 0.00000 0.23525 25 3S 0.00000 0.05644 0.00000 0.00000 -0.65178 26 4PX 0.00000 0.00000 0.04421 0.00000 0.00000 27 4PY 0.00000 0.00000 0.00000 0.04421 0.00000 28 4PZ 0.00000 -0.04735 0.00000 0.00000 -0.10025 29 5PX 0.00000 0.00000 -0.05274 0.00000 0.00000 30 5PY 0.00000 0.00000 0.00000 -0.05274 0.00000 31 5PZ 0.00000 -0.08808 0.00000 0.00000 0.19553 32 6PX 0.00000 0.00000 -0.05072 0.00000 0.00000 33 6PY 0.00000 0.00000 0.00000 -0.05072 0.00000 34 6PZ 0.00000 -0.00310 0.00000 0.00000 0.04830 35 7D 0 0.00000 -0.60831 0.00000 0.00000 -0.19122 36 7D+1 0.00000 0.00000 0.63699 0.00000 0.00000 37 7D-1 0.00000 0.00000 0.00000 0.63699 0.00000 38 7D+2 -0.63722 0.00000 0.00000 0.00000 0.00000 39 7D-2 0.00000 0.00000 0.00000 0.00000 0.00000 40 8D 0 0.00000 -0.20089 0.00000 0.00000 -0.08222 41 8D+1 0.00000 0.00000 0.20061 0.00000 0.00000 42 8D-1 0.00000 0.00000 0.00000 0.20061 0.00000 43 8D+2 -0.16263 0.00000 0.00000 0.00000 0.00000 44 8D-2 0.00000 0.00000 0.00000 0.00000 0.00000 *********************************************************************** From owner-chemistry@ccl.net Wed Feb 26 22:19:00 2014 From: "Andrew Yeung andrew.yeung%x%chem.tamu.edu" To: CCL Subject: CCL: Enthalpy vs free energy of activation? Message-Id: <-49811-140226221744-21966-2shA/bRsWCgR6UiiMBhDUg#,#server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 Feb 2014 21:17:41 -0600 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung : chem.tamu.edu] Hi all I recall that some authors recommend that enthalpy of activation be used, instead of free energy of activation. Does anybody have a reference handy? Thanks! -- Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 Fax: 979 845 0158