From owner-chemistry@ccl.net Fri May 29 01:34:00 2009 From: "Neha Gandhi n.gandhiau]_[gmail.com" To: CCL Subject: CCL: J coupling constant calculation Message-Id: <-39398-090529013118-23796-mNYTzy0WLT3Vuacf3R6q4w[#]server.ccl.net> X-Original-From: Neha Gandhi Content-Type: multipart/alternative; boundary=0016e64dd4cee3e99e046b064adc Date: Fri, 29 May 2009 13:24:37 +0800 MIME-Version: 1.0 Sent to CCL by: Neha Gandhi [n.gandhiau===gmail.com] --0016e64dd4cee3e99e046b064adc Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi List, I was wondering if there is a program/script to calculate theorectical Jcoupling from the AMBER or GROMACS simulations? How can we determine the conformational equlibrium (%) from the MD simulations? Help is appreciated. Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 --0016e64dd4cee3e99e046b064adc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi List,

I was wondering if there is a program/script to calculate theorectical Jcoupling from the AMBER or GROMACS simulations? How can we determine the conformational equlibrium (%) from the MD simulations?

Help is appreciated.

Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
--0016e64dd4cee3e99e046b064adc-- From owner-chemistry@ccl.net Fri May 29 03:21:01 2009 From: "Jens Spanget-Larsen spanget###ruc.dk" To: CCL Subject: CCL:G: questions about TDDFT calculation Message-Id: <-39399-090529032031-25373-LE9VlaKwUYUrgKq2h2tAXg__server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 29 May 2009 09:20:25 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget|,|ruc.dk] Dear Kerwin, the notation in the square brackets indicates the orbitals involved in the one-electron promotion. The numbering of the occupied MOs is indicated with positive integers, starting with HOMO as number 1, SHOMO as number 2, and so forth. Numbering of unoccupied MOs is similar, but with negative integers, starting with LUMO as number -1, SLUMO as -2, etc. This is a very practical numbering scheme: The HOMO --> LUMO excitation is always [ 1,-1 ], SHOMO --> LUMO is [ 2,-1 ], etc. By the way, I forgot an obvious factor of one hundred in the calculation of the percentage in my previous message: Percentage contribution = 2*(C^2)*100. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget!=!ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Kerwin D Dobbs wrote: > > Hi Jens, > > I'm just curious ... what is the notation in square brackets to the > right of the percentages? > > Kerwin > ======================================== > Kerwin Dobbs, Computational Chemist > DuPont CR&D > Information & Computing Technologies > Experimental Station, P O Box 80320 > Wilmington DE 19880-0320 > Kerwin.D.Dobbs!=!usa.dupont.com > http://www.linkedin.com/in/kerwindobbs > > owner-chemistry+kerwin.d.dobbs==usa.dupont.com!=!ccl.net wrote on > 05/28/2009 11:03:29 AM: > > > > > Sent to CCL by: Jens Spanget-Larsen [spanget%ruc.dk] > > > > Hello Noel and Anindita! > > > > Regarding Gaussian TD-DFT output: In case the TD calculation is > based on > > a closed shell ground state representation, computation of the > > percentages is straight forward. If the printed coefficient is given by > > C, then the percentage is twice the square of C, i.e., 2*C^2. The > factor > > 2 is due to the circumstance that Gaussian prints the coefficients of > > microstates, not spin-adapted configurations (if I understand > > correctly!). I use a small utility program to add the percentages, if > > larger than 10%, to the output file, see below. The situation is more > > complicated in the case of an unrestricted open-shell calculation, > where > > this procedure will not work. > > > > Yours, Jens >--< > > ___________ > > > > Excitation energies and oscillator strengths: > > > > Excited State 1: Singlet-B1U 28.31005 1000/cm 353.23 nm > f=1.9822 > > 73 -> 74 0.64930 84% [ 1,-1 ] > > > > Excited State 2: Singlet-AG 35.42708 1000/cm 282.27 nm > f=0.0000 > > 72 -> 74 0.61806 76% [ 2,-1 ] > > 73 -> 75 -0.32572 21% [ 1,-2 ] > > > > Excited State 3: Singlet-B2U 36.18604 1000/cm 276.35 nm > f=0.0002 > > 69 -> 74 0.43019 37% [ 5,-1 ] > > 73 -> 76 0.51753 54% [ 1,-3 ] > > 73 -> 78 -0.21135 > > > > ------------------------------------------------------ > > JENS SPANGET-LARSEN Office: +45 4674 2710 > > Dept. of Science (18.1) Fax: +45 4674 3011 > > Roskilde University Mobile: +45 2320 6246 > > P.O.Box 260 E-Mail: spanget.:.ruc.dk > > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget > > ------------------------------------------------------ > > > > > > > > Noel M O Boyle baoilleach::gmail.com wrote: > > > Sent to CCL by: "Noel M O Boyle" [baoilleach^gmail.com] > > > Hello Anindita, > > > > > > You should probably use the latest version of GaussSum (2.1.6) to > > see whether the problem has been fixed. > > > > > > Regarding the general problem, it is not possible to accurately > > calculate the % contribution of each singly-excited configuration to > > a particular transition from the output of a Gaussian TDDFT > > calculation. As a result, the sum of the squares of the > > contributions will not add to 1.0 exactly. Note that this is not the > > case for the TDDFT implementations in several other QM programs (I > > don't recall the details). > > > > > > BTW, like many (but not all) software discussed on this list, > > GaussSum provides a mailing list for questions: > gausssum-help[a]lists.sf.net > > > > > > Regards, > > > Noel (developer of GaussSum) > > > > > > > > > > > >> "Anindita De de.anindita++gmail.com" wrote: > > >> > > >> Sent to CCL by: "Anindita De" [de.anindita],[gmail.com] > > >> Hello, > > >> > > >> I am a beginner in TDDFT calculation. I want to generate a UV- > > visible spectram and I am using Gaussian 03 for the calculation. I > > have following question > > >> > > >> (i) how to calculate the percentage contribution of each > > transition in UV-Vis spectra ? > > >> > > >> (ii) right now I am using GaussSum programme to plot the spectra. > > Some time it gives contribution more that 100%. Is it correct? > > >> > > >> (iii)I want to do calculation for a dimeric system having two > > unpaired electron in each metal center. Is it better to do > > calculation considering closed shell system? > > >> > > >> I am really confused about these things. Please someone help me. > > >> > > >> Regards, > > >> > > >> Anindita > This communication is for use by the intended recipient and contains > information that may be Privileged, confidential or copyrighted under > applicable law. If you are not the intended recipient, you are hereby > formally notified that any use, copying or distribution of this e-mail, > in whole or in part, is strictly prohibited. Please notify the sender by > return e-mail and delete this e-mail from your system. Unless explicitly > and conspicuously designated as "E-Contract Intended", this e-mail does > not constitute a contract offer, a contract amendment, or an acceptance > of a contract offer. This e-mail does not constitute a consent to the > use of sender's contact information for direct marketing purposes or for > transfers of data to third parties. > > Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean > > http://www.DuPont.com/corp/email_disclaimer.html > From owner-chemistry@ccl.net Fri May 29 05:52:01 2009 From: "Noel M O Boyle baoilleach a gmail.com" To: CCL Subject: CCL:G: questions about TDDFT calculation Message-Id: <-39400-090529053052-3180-q7WCQBJchYjE5tu8ipngBA*server.ccl.net> X-Original-From: "Noel M O Boyle" Date: Fri, 29 May 2009 05:30:46 -0400 Sent to CCL by: "Noel M O Boyle" [baoilleach-.-gmail.com] Hello Jens, The procedure you describe is the same as in GaussSum, and I used to believe that the contributions added to 100% until I was corrected on this very list. Unfortunately, I cannot find the post now but it contained a very nice counterexample. Here is a weaker counterexample; the lowest energy transition of benzene at the B3LYP/3-21G level of theory: Excited State 1: Singlet-?Sym 5.6887 eV 217.95 nm f=0.0000 10 -> 33 0.01232 11 -> 34 -0.01232 13 -> 36 -0.01093 14 -> 24 0.01465 20 -> 23 0.50927 21 -> 22 0.50927 The final two configurations both contribute 52%. One might suggest that all the figures should be scaled by the total sum, but the total sum is only known approximinately (even if IOP(9/40=2) is used). I leave it to the user to decide what to do. - Noel > "Jens Spanget-Larsen spanget---ruc.dk" wrote: > > Sent to CCL by: Jens Spanget-Larsen [spanget%ruc.dk] > > Hello Noel and Anindita! > > Regarding Gaussian TD-DFT output: In case the TD calculation is based on > a closed shell ground state representation, computation of the > percentages is straight forward. If the printed coefficient is given by > C, then the percentage is twice the square of C, i.e., 2*C^2. The factor > 2 is due to the circumstance that Gaussian prints the coefficients of > microstates, not spin-adapted configurations (if I understand > correctly!). I use a small utility program to add the percentages, if > larger than 10%, to the output file, see below. The situation is more > complicated in the case of an unrestricted open-shell calculation, where > this procedure will not work. > > Yours, Jens >--< > ___________ > > Excitation energies and oscillator strengths: > > Excited State 1: Singlet-B1U 28.31005 1000/cm 353.23 nm f=1.9822 > 73 -> 74 0.64930 84% [ 1,-1 ] > > Excited State 2: Singlet-AG 35.42708 1000/cm 282.27 nm f=0.0000 > 72 -> 74 0.61806 76% [ 2,-1 ] > 73 -> 75 -0.32572 21% [ 1,-2 ] > > Excited State 3: Singlet-B2U 36.18604 1000/cm 276.35 nm f=0.0002 > 69 -> 74 0.43019 37% [ 5,-1 ] > 73 -> 76 0.51753 54% [ 1,-3 ] > 73 -> 78 -0.21135 > > ------------------------------------------------------ > JENS SPANGET-LARSEN Office: +45 4674 2710 > Dept. of Science (18.1) Fax: +45 4674 3011 > Roskilde University Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget=-=ruc.dk > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget > ------------------------------------------------------ > > > > Noel M O Boyle baoilleach::gmail.com wrote: > > Sent to CCL by: "Noel M O Boyle" [baoilleach^gmail.com] > > Hello Anindita, > > > > You should probably use the latest version of GaussSum (2.1.6) to see whether the problem has been fixed. > > > > Regarding the general problem, it is not possible to accurately calculate the % contribution of each singly-excited configuration to a particular transition from the output of a Gaussian TDDFT calculation. As a result, the sum of the squares of the contributions will not add to 1.0 exactly. Note that this is not the case for the TDDFT implementations in several other QM programs (I don't recall the details). > > > > BTW, like many (but not all) software discussed on this list, GaussSum provides a mailing list for questions: gausssum-help[a]lists.sf.net > > > > Regards, > > Noel (developer of GaussSum) > > > > > > > >> "Anindita De de.anindita++gmail.com" wrote: > >> > >> Sent to CCL by: "Anindita De" [de.anindita],[gmail.com] > >> Hello, > >> > >> I am a beginner in TDDFT calculation. I want to generate a UV-visible spectram and I am using Gaussian 03 for the calculation. I have following question > >> > >> (i) how to calculate the percentage contribution of each transition in UV-Vis spectra ? > >> > >> (ii) right now I am using GaussSum programme to plot the spectra. Some time it gives contribution more that 100%. Is it correct? > >> > >> (iii)I want to do calculation for a dimeric system having two unpaired electron in each metal center. Is it better to do calculation considering closed shell system? > >> > >> I am really confused about these things. Please someone help me. > >> > >> Regards, > >> > >> Anindita > >> > >> > >> > > > > > > > > From owner-chemistry@ccl.net Fri May 29 09:29:01 2009 From: "Karol Marek Langner karol.langner-$-gmail.com" To: CCL Subject: CCL:G: Huge Number of Basis Functions Message-Id: <-39401-090528154026-16946-D8BDHbpVel+OanK1CUvgGg^server.ccl.net> X-Original-From: "Karol Marek Langner" Date: Thu, 28 May 2009 15:40:22 -0400 Sent to CCL by: "Karol Marek Langner" [karol.langner!A!gmail.com] Esteban, I have done comparable calculations recently (27 atoms/2300 atomic orbitals, 280 atoms/2200 atomic orbitals), so you are not dreaming. However, I used GAMESS-US and had a pretty large computer cluster with a lot of RAM at my disposal. Also, I'm not sure if g03 would scale well above a couple of tens of CPUs for single point energy. I hear Turbomole is much better at scaling, although in my case GAMESS-US did fine. Cheers, Karol > "Esteban Gabriel Vega Hissi egvega+*+gmail.com" wrote: > Hi CCL readers, > > Is it possible to perform a single point (energy) calculation with > gaussian03 of a 78 atoms system with about 2800 basis functions or am I > dreaming? > The level of calculation I require is: MP2(FC)/aug-cc-pVTZ > > I hope you can help me. > Thanks in advance > Best wishes > > Biochemist Esteban Gabriel Vega Hissi > UNSL > Argentina From owner-chemistry@ccl.net Fri May 29 10:04:00 2009 From: "nand kishor gour chintu01chem..gmail.com" To: CCL Subject: CCL:G: chemistry Message-Id: <-39402-090529043008-23396-3dj57W49Xcm0YkNL5nxHag||server.ccl.net> X-Original-From: "nand kishor gour" Date: Fri, 29 May 2009 04:30:04 -0400 Sent to CCL by: "nand kishor gour" [chintu01chem{=}gmail.com] i wants to calculate some phyico-chemical prpoerties of compounds at other than room temperature in gas phase using Gaussian View, how submit such jobs ? Nandikshor