From owner-chemistry@ccl.net Wed Sep 17 08:12:10 2008 From: "Alejandro Pisanty apisan^_^servidor.unam.mx" To: CCL Subject: CCL: CCL operates on a portable generator at this moment Message-Id: <-37760-080916194633-30599-XWXgvD4UZrdoGA5ohIEz0g|*|server.ccl.net> X-Original-From: Alejandro Pisanty Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 16 Sep 2008 22:44:29 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Alejandro Pisanty [apisan:-:servidor.unam.mx] Jan, I consider your efforts heroic. An inhabitant of the CCL since 1991 (that's right, almost 18 years now) I've been witness of the many times you've saved the CCL from massive, irreversible disaster. I've posted a note in this respect in my blog, both in English and Spanish; it is in http://pisanty.blogspot.com. Yours (with hat off), Alejandro Pisanty . . . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty UNAM, Av. Universidad 3000, 04510 Mexico DF Mexico Tels. +52-(1)-55-5105-6044, +52-(1)-55-5418-3732 *Mi blog/My blog: http://pisanty.blogspot.com *LinkedIn profile: http://www.linkedin.com/in/pisanty *Unete al grupo UNAM en LinkedIn, http://www.linkedin.com/e/gis/22285/4A106C0C8614 ---->> Unete a ISOC Mexico, http://www.isoc.org Participa en ICANN, http://www.icann.org . . . . . . . . . . . . . . . . . . . . . . . . . . On Tue, 16 Sep 2008, Jan Labanowski janl a speakeasy.net wrote: > Date: Tue, 16 Sep 2008 13:49:25 EDT > From: Jan Labanowski janl a speakeasy.net > Reply-To: CCL Subscribers > To: "Pisanty, Alejandro " > Subject: CCL: CCL operates on a portable generator at this moment > > > Sent to CCL by: Jan Labanowski [janl..speakeasy.net] > Dear CCL, > > I am sorry for the outage of CCL... > About 3pm EDT (NY Time) on Sunday I took my kid to a practice North of > Columbus. Once we arrived, out of the blue (no warnings, no nothing) > the trees started to fall down and I had a hard time keeping my car on > the road. I arrived home at 5pm and the power was out. We are talking > Sunday afternoon here... Everything is closed... Most crews are away to > save victims of Ike in the South. Supposedly nobody knew that this > thing will happen, and heavy wind warnings were issued at about that > time when it happened. They did not have such thing in Central Ohio > supposedly for over 40 years. I personally do not remember the power > outage that lasted more than couple hours. In most of the City > where the power lines are above the ground the electricity is gone. > Most of the gas stations on Sunday evening were out of business since > they were out of power. > > You can see up to date information at: > > http://www.aepohio.com/News/outages/default.asp > > Next morning (Monday) the generators were sold out within 15 minutes >> from the moment the stores were opened. I also heard that they did not > have many of them left in Ohio, since they moved them a few days > ago to the South where they are in short supply. There is a State > of Emergency in Ohio, the Schools are closed, etc. Luckily, I cut my > old decaying oak tree last summer. If I waited longer, it would be now > on my roof. > > The estimate is that they will fix the power in a week. They are doing > a good job, and numbers at the site given above were much higher than > they are now. I managed to get the generator (not the nice silent one, > but the noisy large monster) and the CCL runs out on it at this moment. > Knowing my luck, I hoped that after I buy the damned generatorm, the power > will be back up when I park in my driveway, but so far I was proven wrong. > > My network connection was also out until about noon on Monday (I could > check it using an inverter in my car) but now it works OK. > > Keep your fingers crossed... > > Jan > Your CCL keeper...> > > From owner-chemistry@ccl.net Wed Sep 17 08:18:01 2008 From: "Jason Stephen D Acchioli jdacchio .. uwsp.edu" To: CCL Subject: CCL:G: Rotation in linear molecules Message-Id: <-37761-080916175908-24467-Q957g9hJnR68YGttXkW4Eg(_)server.ccl.net> X-Original-From: "Jason Stephen D Acchioli" Date: Tue, 16 Sep 2008 17:59:03 -0400 Sent to CCL by: "Jason Stephen D Acchioli" [jdacchio(!)uwsp.edu] Hi all, I have a student who's going to be constructing a Walsh diagram analyzing the effect of rotation on the energy of delta and pi orbitals in a naked Mo2 center. What's the best way to do a rigid PES on this type of molecule? He's tried using two dummy atoms, and twisting a dihedral, but G03 doesn't like it. Any suggestions? Thanks, Jason Jason D'Acchioli Assistant Professor of Chemistry University of Wisconsin-Stevens Point 2001 Fourth Avenue Stevens Point, WI 54481 http://chemdept-nmr.uwsp.edu/~jdacchio From owner-chemistry@ccl.net Wed Sep 17 11:05:00 2008 From: "Igor Filippov Contr igorf_._helix.nih.gov" To: CCL Subject: CCL: Again, about the CCL attached to a lawn mower... Message-Id: <-37762-080917102240-13665-vjSbnOJMTPsHbRdnf1Sn9g##server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 16 Sep 2008 23:15:27 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf.:.helix.nih.gov] Jan, This is really beyond what anybody could have done! Hope life will come back to normal in Columbus soon. Best wishes, Igor On Tue, 2008-09-16 at 19:12 -0400, Jan Labanowski janl|speakeasy.net wrote: > Sent to CCL by: Jan Labanowski [janl]![speakeasy.net] > > Dear CCL > > It is me again... > My current experience with the generator that runs the CCL shows that > this thing will run about 6 hours on a tank of gasoline (5 gallons). > They advertised it as 9 hours, but they probably forgot to add that it > is for the case when you do not attach anything to this thing and just > run it to power your watch or just dry, for the fun of doing it. I am > refilling it "on the run" (which is of course a big "No, No..."). But > filling up this thing with gas during the night would be a challenge. > Moreover, it is now hot like hell (if you believe in it, but you better > believe in it, when you check the latest stock prices) and I am not > sure if this device is made to run 24/7. Probably, theoretically, but... > So, unless they fix the power by late evening today, I will be shutting > down the computers for the night and restart the operation in the morning. > > Since messages that you send are queued on non-delivery for up to 4 days, > if you send something to CCL when it is down, your machine should retry > delivery and post it when CCL is past its nocturnal inactivity. Another > option is to check if CCL home page ( http://www.ccl.net ) is up before > posting. > > Sorry about it but I wish I could do more. > > Jan > The part-time CCL keeper... > > > > -> > -- Igor Filippov [Contr] From owner-chemistry@ccl.net Wed Sep 17 11:49:01 2008 From: "Stephen Wilson quantumsystems*o*gmail.com" To: CCL Subject: CCL: New book: Hybrid Methods of Molecular Modeling Message-Id: <-37763-080917114352-22708-5QWkwUfoZ4nL+CFPbaq+LQ~~server.ccl.net> X-Original-From: "Stephen Wilson" Date: Wed, 17 Sep 2008 11:43:47 -0400 Sent to CCL by: "Stephen Wilson" [quantumsystems*|*gmail.com] Hybrid Methods of Molecular Modeling (346 p.) by Andrei L. Tchougreeff Moscow State (Lomonosov) University has been published by Springer in the Progress in Theoretical Chemistry & Physics series. For details go to: http://www.springer.com/chemistry/book/978-1-4020-8188-0 For details of the PTCP series visit: http://www.springer.com/series/6464 From owner-chemistry@ccl.net Wed Sep 17 15:39:01 2008 From: "Tamas Gunda tgunda2]|[puma.unideb.hu" To: CCL Subject: CCL: bondAtomProblem Message-Id: <-37764-080917081720-9761-9QYB19HZnzz4q61cBDwPZg(a)server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 17 Sep 2008 09:30:11 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2:-:puma.unideb.hu] There is problem in the file structure concerning to position of the atom name section. In the atom name section (cols 13-16) the numbering of hydrogens runs over 100 (H100 etc) and the rightmost digit occupies column 17, which is reserved for the indication of alternate locations. This might easily confuse the program when interpreting the structure. As the numeral part of the atom names are usually not very important, you should try the replece the third digit manually. It is very easy with an appropriate asci text editor. However, here it is in corrected form. Does it work? -------------------- ATOM 1 O1 MOL 1 0.483 3.644 -6.151 ATOM 2 H2 MOL 1 0.276 2.895 -6.696 ATOM 3 C3 MOL 1 0.521 3.200 -4.826 ATOM 4 H4 MOL 1 1.164 2.302 -4.726 ATOM 5 H5 MOL 1 1.014 4.038 -4.297 ATOM 6 C6 MOL 1 -0.859 2.900 -4.197 ATOM 7 O7 MOL 1 -1.505 4.168 -4.052 ATOM 8 H8 MOL 1 -0.676 2.470 -3.180 ATOM 9 C9 MOL 1 -1.725 1.910 -5.020 ATOM 10 O10 MOL 1 -1.106 0.628 -4.921 ATOM 11 H11 MOL 1 -1.810 2.237 -6.089 ATOM 12 C12 MOL 1 -3.144 1.783 -4.392 ATOM 13 O13 MOL 1 -4.022 1.056 -5.224 ATOM 14 H14 MOL 1 -3.597 0.222 -5.428 ATOM 15 H15 MOL 1 -3.083 1.278 -3.396 ATOM 16 C16 MOL 1 -3.763 3.196 -4.243 ATOM 17 O17 MOL 1 -4.980 3.190 -3.523 ATOM 18 H18 MOL 1 -5.519 2.506 -3.900 ATOM 19 H19 MOL 1 -3.963 3.633 -5.254 ATOM 20 C20 MOL 1 -2.788 4.146 -3.489 ATOM 21 H21 MOL 1 -3.112 5.214 -3.554 ATOM 22 O22 MOL 1 -2.561 3.717 -2.162 ATOM 23 C23 MOL 1 -2.883 4.658 -1.137 ATOM 24 C24 MOL 1 -1.587 4.924 -0.325 ATOM 25 O25 MOL 1 -1.857 5.671 0.865 ATOM 26 C26 MOL 1 -0.518 5.734 -1.094 ATOM 27 O27 MOL 1 -0.952 6.968 -1.588 ATOM 28 H28 MOL 1 -1.536 6.794 -2.317 ATOM 29 H29 MOL 1 0.312 6.017 -0.420 ATOM 30 H30 MOL 1 -0.103 5.104 -1.907 ATOM 31 H31 MOL 1 -1.124 3.946 -0.040 ATOM 32 H32 MOL 1 -3.288 5.608 -1.572 ATOM 33 C33 MOL 1 -3.960 3.983 -0.239 ATOM 34 O34 MOL 1 -5.215 3.926 -0.882 ATOM 35 H35 MOL 1 -5.077 3.534 -1.746 ATOM 36 H36 MOL 1 -3.643 2.945 0.032 ATOM 37 C37 MOL 1 -4.170 4.832 1.041 ATOM 38 O38 MOL 1 -4.996 4.196 1.996 ATOM 39 H39 MOL 1 -5.755 3.869 1.530 ATOM 40 H40 MOL 1 -4.642 5.811 0.776 ATOM 41 C41 MOL 1 -2.808 5.122 1.736 ATOM 42 H42 MOL 1 -2.901 5.902 2.531 ATOM 43 O43 MOL 1 -2.196 3.935 2.195 ATOM 44 C44 MOL 1 -1.874 3.900 3.585 ATOM 45 C45 MOL 1 -2.675 2.712 4.195 ATOM 46 C46 MOL 1 -2.183 2.455 5.642 ATOM 47 O47 MOL 1 -2.733 1.283 6.208 ATOM 48 H48 MOL 1 -3.668 1.315 6.047 ATOM 49 H49 MOL 1 -2.459 3.317 6.299 ATOM 50 O50 MOL 1 -4.052 3.007 4.291 ATOM 51 H51 MOL 1 -4.343 3.298 3.425 ATOM 52 H52 MOL 1 -2.542 1.793 3.571 ATOM 53 H53 MOL 1 -2.165 4.856 4.092 ATOM 54 C54 MOL 1 -0.349 3.644 3.705 ATOM 55 C55 MOL 1 0.527 4.842 3.267 ATOM 56 O56 MOL 1 0.238 6.050 3.908 ATOM 57 H57 MOL 1 -0.576 6.377 3.546 ATOM 58 H58 MOL 1 1.585 4.666 3.534 ATOM 59 H59 MOL 1 0.462 4.951 2.165 ATOM 60 H60 MOL 1 -0.069 2.774 3.060 ATOM 61 O61 MOL 1 0.033 3.359 5.056 ATOM 62 C62 MOL 1 -0.636 2.295 5.674 ATOM 63 H63 MOL 1 -0.235 2.314 6.716 ATOM 64 O64 MOL 1 -0.218 1.166 4.938 ATOM 65 C65 MOL 1 0.558 0.201 5.647 ATOM 66 C66 MOL 1 -0.237 -1.138 5.592 ATOM 67 C67 MOL 1 0.666 -2.288 6.105 ATOM 68 O68 MOL 1 0.085 -3.565 5.925 ATOM 69 H69 MOL 1 -0.798 -3.515 6.263 ATOM 70 H70 MOL 1 0.874 -2.154 7.196 ATOM 71 O71 MOL 1 -1.369 -1.120 6.443 ATOM 72 H72 MOL 1 -1.862 -0.322 6.248 ATOM 73 H73 MOL 1 -0.572 -1.345 4.544 ATOM 74 H74 MOL 1 0.715 0.508 6.714 ATOM 75 C75 MOL 1 1.910 0.063 4.898 ATOM 76 C76 MOL 1 2.836 1.293 5.044 ATOM 77 O77 MOL 1 3.114 1.670 6.361 ATOM 78 H78 MOL 1 2.331 2.078 6.712 ATOM 79 H79 MOL 1 2.406 2.139 4.470 ATOM 80 H80 MOL 1 3.839 1.073 4.633 ATOM 81 H81 MOL 1 1.714 -0.078 3.806 ATOM 82 O82 MOL 1 2.669 -1.052 5.377 ATOM 83 C83 MOL 1 2.025 -2.295 5.345 ATOM 84 H84 MOL 1 2.769 -2.978 5.823 ATOM 85 O85 MOL 1 1.845 -2.547 3.967 ATOM 86 C86 MOL 1 2.568 -3.657 3.436 ATOM 87 C87 MOL 1 1.509 -4.656 2.886 ATOM 88 C88 MOL 1 2.225 -5.760 2.069 ATOM 89 O89 MOL 1 1.325 -6.616 1.394 ATOM 90 H90 MOL 1 0.677 -6.890 2.031 ATOM 91 H91 MOL 1 2.856 -6.388 2.746 ATOM 92 O92 MOL 1 0.821 -5.315 3.927 ATOM 93 H93 MOL 1 0.494 -4.642 4.525 ATOM 94 H94 MOL 1 0.766 -4.119 2.244 ATOM 95 H95 MOL 1 3.186 -4.155 4.228 ATOM 96 C96 MOL 1 3.461 -3.122 2.285 ATOM 97 C97 MOL 1 4.645 -2.250 2.762 ATOM 98 O98 MOL 1 5.480 -2.852 3.708 ATOM 99 H99 MOL 1 5.009 -2.868 4.534 ATOM 100 H10 MOL 1 5.334 -2.040 1.923 ATOM 101 H10 MOL 1 4.252 -1.282 3.137 ATOM 102 H10 MOL 1 2.840 -2.494 1.598 ATOM 103 O10 MOL 1 4.045 -4.189 1.530 ATOM 104 C10 MOL 1 3.152 -5.125 0.991 ATOM 105 H10 MOL 1 3.827 -5.882 0.524 ATOM 106 O10 MOL 1 2.419 -4.374 0.047 ATOM 107 C10 MOL 1 2.557 -4.769 -1.318 ATOM 108 C10 MOL 1 1.134 -5.156 -1.819 ATOM 109 C10 MOL 1 1.171 -5.360 -3.355 ATOM 110 O11 MOL 1 -0.114 -5.536 -3.919 ATOM 111 H11 MOL 1 -0.566 -6.174 -3.381 ATOM 112 H11 MOL 1 1.781 -6.265 -3.604 ATOM 113 O11 MOL 1 0.700 -6.382 -1.272 ATOM 114 H11 MOL 1 0.824 -6.334 -0.323 ATOM 115 H11 MOL 1 0.398 -4.358 -1.551 ATOM 116 H11 MOL 1 3.250 -5.643 -1.421 ATOM 117 C11 MOL 1 3.083 -3.540 -2.106 ATOM 118 C11 MOL 1 4.542 -3.152 -1.772 ATOM 119 O11 MOL 1 5.471 -4.189 -1.890 ATOM 120 H12 MOL 1 5.348 -4.767 -1.146 ATOM 121 H12 MOL 1 4.917 -2.401 -2.492 ATOM 122 H12 MOL 1 4.573 -2.703 -0.758 ATOM 123 H12 MOL 1 2.440 -2.654 -1.877 ATOM 124 O12 MOL 1 3.058 -3.778 -3.516 ATOM 125 C12 MOL 1 1.818 -4.133 -4.062 ATOM 126 H12 MOL 1 2.066 -4.351 -5.130 ATOM 127 O12 MOL 1 1.035 -2.965 -3.913 ATOM 128 C12 MOL 1 0.634 -2.336 -5.131 ATOM 129 H12 MOL 1 1.030 -2.903 -6.020 ATOM 130 C13 MOL 1 -0.921 -2.336 -5.131 ATOM 131 O13 MOL 1 -1.436 -3.622 -5.404 ATOM 132 H13 MOL 1 -1.037 -4.226 -4.776 ATOM 133 H13 MOL 1 -1.307 -1.990 -4.139 ATOM 134 C13 MOL 1 -1.441 -1.410 -6.258 ATOM 135 O13 MOL 1 -2.842 -1.225 -6.217 ATOM 136 H13 MOL 1 -3.232 -2.085 -6.123 ATOM 137 H13 MOL 1 -1.180 -1.837 -7.258 ATOM 138 C13 MOL 1 -0.787 -0.002 -6.144 ATOM 139 H13 MOL 1 -1.003 0.635 -7.036 ATOM 140 O14 MOL 1 0.612 -0.061 -6.129 ATOM 141 C14 MOL 1 1.210 -0.894 -5.131 ATOM 142 H14 MOL 1 1.050 -0.420 -4.131 ATOM 143 C14 MOL 1 2.725 -0.877 -5.443 ATOM 144 H14 MOL 1 3.101 0.156 -5.554 ATOM 145 H14 MOL 1 3.274 -1.355 -4.606 ATOM 146 O14 MOL 1 3.081 -1.477 -6.656 ATOM 147 H14 MOL 1 2.665 -2.334 -6.676 CONECT 1 2 3 CONECT 2 1 CONECT 3 1 4 5 6 CONECT 4 3 CONECT 5 3 CONECT 6 3 7 8 9 CONECT 7 6 20 CONECT 8 6 CONECT 9 6 10 11 12 CONECT 10 9 138 CONECT 11 9 CONECT 12 9 13 15 16 CONECT 13 12 14 CONECT 14 13 CONECT 15 12 CONECT 16 12 17 19 20 CONECT 17 16 18 CONECT 18 17 CONECT 19 16 CONECT 20 7 16 21 22 CONECT 21 20 CONECT 22 20 23 CONECT 23 22 24 32 33 CONECT 24 23 25 26 31 CONECT 25 24 41 CONECT 26 24 27 29 30 CONECT 27 26 28 CONECT 28 27 CONECT 29 26 CONECT 30 26 CONECT 31 24 CONECT 32 23 CONECT 33 23 34 36 37 CONECT 34 33 35 CONECT 35 34 CONECT 36 33 CONECT 37 33 38 40 41 CONECT 38 37 39 CONECT 39 38 CONECT 40 37 CONECT 41 25 37 42 43 CONECT 42 41 CONECT 43 41 44 CONECT 44 43 45 53 54 CONECT 45 44 46 50 52 CONECT 46 45 47 49 62 CONECT 47 46 48 CONECT 48 47 CONECT 49 46 CONECT 50 45 51 CONECT 51 50 CONECT 52 45 CONECT 53 44 CONECT 54 44 55 60 61 CONECT 55 54 56 58 59 CONECT 56 55 57 CONECT 57 56 CONECT 58 55 CONECT 59 55 CONECT 60 54 CONECT 61 54 62 CONECT 62 46 61 63 64 CONECT 63 62 CONECT 64 62 65 CONECT 65 64 66 74 75 CONECT 66 65 67 71 73 CONECT 67 66 68 70 83 CONECT 68 67 69 CONECT 69 68 CONECT 70 67 CONECT 71 66 72 CONECT 72 71 CONECT 73 66 CONECT 74 65 CONECT 75 65 76 81 82 CONECT 76 75 77 79 80 CONECT 77 76 78 CONECT 78 77 CONECT 79 76 CONECT 80 76 CONECT 81 75 CONECT 82 75 83 CONECT 83 67 82 84 85 CONECT 84 83 CONECT 85 83 86 CONECT 86 85 87 95 96 CONECT 87 86 88 92 94 CONECT 88 87 89 91 104 CONECT 89 88 90 CONECT 90 89 CONECT 91 88 CONECT 92 87 93 CONECT 93 92 CONECT 94 87 CONECT 95 86 CONECT 96 86 97 102 103 CONECT 97 96 98 100 101 CONECT 98 97 99 CONECT 99 98 CONECT 100 97 CONECT 101 97 CONECT 102 96 CONECT 103 96 104 CONECT 104 88 103 105 106 CONECT 105 104 CONECT 106 104 107 CONECT 107 106 108 116 117 CONECT 108 107 109 113 115 CONECT 109 108 110 112 125 CONECT 110 109 111 CONECT 111 110 CONECT 112 109 CONECT 113 108 114 CONECT 114 113 CONECT 115 108 CONECT 116 107 CONECT 117 107 118 123 124 CONECT 118 117 119 121 122 CONECT 119 118 120 CONECT 120 119 CONECT 121 118 CONECT 122 118 CONECT 123 117 CONECT 124 117 125 CONECT 125 109 124 126 127 CONECT 126 125 CONECT 127 125 128 CONECT 128 127 129 130 141 CONECT 129 128 CONECT 130 128 131 133 134 CONECT 131 130 132 CONECT 132 131 CONECT 133 130 CONECT 134 130 135 137 138 CONECT 135 134 136 CONECT 136 135 CONECT 137 134 CONECT 138 10 134 139 140 CONECT 139 138 CONECT 140 138 141 CONECT 141 128 140 142 143 CONECT 142 141 CONECT 143 141 144 145 146 CONECT 144 143 CONECT 145 143 CONECT 146 143 147 CONECT 147 146 ----------------------------------- ----- Original Message ----- Subject: CCL: bondAtomProblem > > Sent to CCL by: "amine amine" [m-22||hotmail.fr] > Hi, > This is my pdb file and i recive: > Bond: Maximum coordination exceeded on .R.A > -- setting atoms pert=true overrides default limits > ATOMS NOT BONDED: .R.A .R.A > !FATAL ERROR---------------------------------------- > !FATAL: In file [atom.c], line 444 > !FATAL: Message: bondAtomProblem found > ! > !ABORTING. > when i make loadpdb file.pdb into leap in amber10, What's the wrong > ------------------------------------------------------------ > ATOM 1 O1 MOL 1 0.483 3.644 -6.151 > ATOM 2 H2 MOL 1 0.276 2.895 -6.696 > ATOM 3 C3 MOL 1 0.521 3.200 -4.826 > ATOM 4 H4 MOL 1 1.164 2.302 -4.726 > ATOM 5 H5 MOL 1 1.014 4.038 -4.297 > ATOM 6 C6 MOL 1 -0.859 2.900 -4.197 > ATOM 7 O7 MOL 1 -1.505 4.168 -4.052 > ATOM 8 H8 MOL 1 -0.676 2.470 -3.180 > ATOM 9 C9 MOL 1 -1.725 1.910 -5.020 > ATOM 10 O10 MOL 1 -1.106 0.628 -4.921 > ATOM 11 H11 MOL 1 -1.810 2.237 -6.089 > ATOM 12 C12 MOL 1 -3.144 1.783 -4.392 > ATOM 13 O13 MOL 1 -4.022 1.056 -5.224 > ATOM 14 H14 MOL 1 -3.597 0.222 -5.428 > ATOM 15 H15 MOL 1 -3.083 1.278 -3.396 > ATOM 16 C16 MOL 1 -3.763 3.196 -4.243 > ATOM 17 O17 MOL 1 -4.980 3.190 -3.523 > ATOM 18 H18 MOL 1 -5.519 2.506 -3.900 > ATOM 19 H19 MOL 1 -3.963 3.633 -5.254 > ATOM 20 C20 MOL 1 -2.788 4.146 -3.489 > ATOM 21 H21 MOL 1 -3.112 5.214 -3.554 > ATOM 22 O22 MOL 1 -2.561 3.717 -2.162 > ATOM 23 C23 MOL 1 -2.883 4.658 -1.137 > ATOM 24 C24 MOL 1 -1.587 4.924 -0.325 > ATOM 25 O25 MOL 1 -1.857 5.671 0.865 > ATOM 26 C26 MOL 1 -0.518 5.734 -1.094 > ATOM 27 O27 MOL 1 -0.952 6.968 -1.588 > ATOM 28 H28 MOL 1 -1.536 6.794 -2.317 > ATOM 29 H29 MOL 1 0.312 6.017 -0.420 > ATOM 30 H30 MOL 1 -0.103 5.104 -1.907 > ATOM 31 H31 MOL 1 -1.124 3.946 -0.040 > ATOM 32 H32 MOL 1 -3.288 5.608 -1.572 > ATOM 33 C33 MOL 1 -3.960 3.983 -0.239 > ATOM 34 O34 MOL 1 -5.215 3.926 -0.882 > ATOM 35 H35 MOL 1 -5.077 3.534 -1.746 > ATOM 36 H36 MOL 1 -3.643 2.945 0.032 > ATOM 37 C37 MOL 1 -4.170 4.832 1.041 > ATOM 38 O38 MOL 1 -4.996 4.196 1.996 > ATOM 39 H39 MOL 1 -5.755 3.869 1.530 > ATOM 40 H40 MOL 1 -4.642 5.811 0.776 > ATOM 41 C41 MOL 1 -2.808 5.122 1.736 > ATOM 42 H42 MOL 1 -2.901 5.902 2.531 > ATOM 43 O43 MOL 1 -2.196 3.935 2.195 > ATOM 44 C44 MOL 1 -1.874 3.900 3.585 > ATOM 45 C45 MOL 1 -2.675 2.712 4.195 > ATOM 46 C46 MOL 1 -2.183 2.455 5.642 > ATOM 47 O47 MOL 1 -2.733 1.283 6.208 > ATOM 48 H48 MOL 1 -3.668 1.315 6.047 > ATOM 49 H49 MOL 1 -2.459 3.317 6.299 > ATOM 50 O50 MOL 1 -4.052 3.007 4.291 > ATOM 51 H51 MOL 1 -4.343 3.298 3.425 > ATOM 52 H52 MOL 1 -2.542 1.793 3.571 > ATOM 53 H53 MOL 1 -2.165 4.856 4.092 > ATOM 54 C54 MOL 1 -0.349 3.644 3.705 > ATOM 55 C55 MOL 1 0.527 4.842 3.267 > ATOM 56 O56 MOL 1 0.238 6.050 3.908 > ATOM 57 H57 MOL 1 -0.576 6.377 3.546 > ATOM 58 H58 MOL 1 1.585 4.666 3.534 > ATOM 59 H59 MOL 1 0.462 4.951 2.165 > ATOM 60 H60 MOL 1 -0.069 2.774 3.060 > ATOM 61 O61 MOL 1 0.033 3.359 5.056 > ATOM 62 C62 MOL 1 -0.636 2.295 5.674 > ATOM 63 H63 MOL 1 -0.235 2.314 6.716 > ATOM 64 O64 MOL 1 -0.218 1.166 4.938 > ATOM 65 C65 MOL 1 0.558 0.201 5.647 > ATOM 66 C66 MOL 1 -0.237 -1.138 5.592 > ATOM 67 C67 MOL 1 0.666 -2.288 6.105 > ATOM 68 O68 MOL 1 0.085 -3.565 5.925 > ATOM 69 H69 MOL 1 -0.798 -3.515 6.263 > ATOM 70 H70 MOL 1 0.874 -2.154 7.196 > ATOM 71 O71 MOL 1 -1.369 -1.120 6.443 > ATOM 72 H72 MOL 1 -1.862 -0.322 6.248 > ATOM 73 H73 MOL 1 -0.572 -1.345 4.544 > ATOM 74 H74 MOL 1 0.715 0.508 6.714 > ATOM 75 C75 MOL 1 1.910 0.063 4.898 > ATOM 76 C76 MOL 1 2.836 1.293 5.044 > ATOM 77 O77 MOL 1 3.114 1.670 6.361 > ATOM 78 H78 MOL 1 2.331 2.078 6.712 > ATOM 79 H79 MOL 1 2.406 2.139 4.470 > ATOM 80 H80 MOL 1 3.839 1.073 4.633 > ATOM 81 H81 MOL 1 1.714 -0.078 3.806 > ATOM 82 O82 MOL 1 2.669 -1.052 5.377 > ATOM 83 C83 MOL 1 2.025 -2.295 5.345 > ATOM 84 H84 MOL 1 2.769 -2.978 5.823 > ATOM 85 O85 MOL 1 1.845 -2.547 3.967 > ATOM 86 C86 MOL 1 2.568 -3.657 3.436 > ATOM 87 C87 MOL 1 1.509 -4.656 2.886 > ATOM 88 C88 MOL 1 2.225 -5.760 2.069 > ATOM 89 O89 MOL 1 1.325 -6.616 1.394 > ATOM 90 H90 MOL 1 0.677 -6.890 2.031 > ATOM 91 H91 MOL 1 2.856 -6.388 2.746 > ATOM 92 O92 MOL 1 0.821 -5.315 3.927 > ATOM 93 H93 MOL 1 0.494 -4.642 4.525 > ATOM 94 H94 MOL 1 0.766 -4.119 2.244 > ATOM 95 H95 MOL 1 3.186 -4.155 4.228 > ATOM 96 C96 MOL 1 3.461 -3.122 2.285 > ATOM 97 C97 MOL 1 4.645 -2.250 2.762 > ATOM 98 O98 MOL 1 5.480 -2.852 3.708 > ATOM 99 H99 MOL 1 5.009 -2.868 4.534 > ATOM 100 H100MOL 1 5.334 -2.040 1.923 > ATOM 101 H101MOL 1 4.252 -1.282 3.137 > ATOM 102 H102MOL 1 2.840 -2.494 1.598 > ATOM 103 O103MOL 1 4.045 -4.189 1.530 > ATOM 104 C104MOL 1 3.152 -5.125 0.991 > ATOM 105 H105MOL 1 3.827 -5.882 0.524 > ATOM 106 O106MOL 1 2.419 -4.374 0.047 > ATOM 107 C107MOL 1 2.557 -4.769 -1.318 > ATOM 108 C108MOL 1 1.134 -5.156 -1.819 > ATOM 109 C109MOL 1 1.171 -5.360 -3.355 > ATOM 110 O110MOL 1 -0.114 -5.536 -3.919 > ATOM 111 H111MOL 1 -0.566 -6.174 -3.381 > ATOM 112 H112MOL 1 1.781 -6.265 -3.604 > ATOM 113 O113MOL 1 0.700 -6.382 -1.272 > ATOM 114 H114MOL 1 0.824 -6.334 -0.323 > ATOM 115 H115MOL 1 0.398 -4.358 -1.551 > ATOM 116 H116MOL 1 3.250 -5.643 -1.421 > ATOM 117 C117MOL 1 3.083 -3.540 -2.106 > ATOM 118 C118MOL 1 4.542 -3.152 -1.772 > ATOM 119 O119MOL 1 5.471 -4.189 -1.890 > ATOM 120 H120MOL 1 5.348 -4.767 -1.146 > ATOM 121 H121MOL 1 4.917 -2.401 -2.492 > ATOM 122 H122MOL 1 4.573 -2.703 -0.758 > ATOM 123 H123MOL 1 2.440 -2.654 -1.877 > ATOM 124 O124MOL 1 3.058 -3.778 -3.516 > ATOM 125 C125MOL 1 1.818 -4.133 -4.062 > ATOM 126 H126MOL 1 2.066 -4.351 -5.130 > ATOM 127 O127MOL 1 1.035 -2.965 -3.913 > ATOM 128 C128MOL 1 0.634 -2.336 -5.131 > ATOM 129 H129MOL 1 1.030 -2.903 -6.020 > ATOM 130 C130MOL 1 -0.921 -2.336 -5.131 > ATOM 131 O131MOL 1 -1.436 -3.622 -5.404 > ATOM 132 H132MOL 1 -1.037 -4.226 -4.776 > ATOM 133 H133MOL 1 -1.307 -1.990 -4.139 > ATOM 134 C134MOL 1 -1.441 -1.410 -6.258 > ATOM 135 O135MOL 1 -2.842 -1.225 -6.217 > ATOM 136 H136MOL 1 -3.232 -2.085 -6.123 > ATOM 137 H137MOL 1 -1.180 -1.837 -7.258 > ATOM 138 C138MOL 1 -0.787 -0.002 -6.144 > ATOM 139 H139MOL 1 -1.003 0.635 -7.036 > ATOM 140 O140MOL 1 0.612 -0.061 -6.129 > ATOM 141 C141MOL 1 1.210 -0.894 -5.131 > ATOM 142 H142MOL 1 1.050 -0.420 -4.131 > ATOM 143 C143MOL 1 2.725 -0.877 -5.443 > ATOM 144 H144MOL 1 3.101 0.156 -5.554 > ATOM 145 H145MOL 1 3.274 -1.355 -4.606 > ATOM 146 O146MOL 1 3.081 -1.477 -6.656 > ATOM 147 H147MOL 1 2.665 -2.334 -6.676 > CONECT 1 2 3 > CONECT 2 1 > CONECT 3 1 4 5 6 > CONECT 4 3 > CONECT 5 3 > CONECT 6 3 7 8 9 > CONECT 7 6 20 > CONECT 8 6 > CONECT 9 6 10 11 12 > CONECT 10 9 138 > CONECT 11 9 > CONECT 12 9 13 15 16 > CONECT 13 12 14 > CONECT 14 13 > CONECT 15 12 > CONECT 16 12 17 19 20 > CONECT 17 16 18 > CONECT 18 17 > CONECT 19 16 > CONECT 20 7 16 21 22 > CONECT 21 20 > CONECT 22 20 23 > CONECT 23 22 24 32 33 > CONECT 24 23 25 26 31 > CONECT 25 24 41 > CONECT 26 24 27 29 30 > CONECT 27 26 28 > CONECT 28 27 > CONECT 29 26 > CONECT 30 26 > CONECT 31 24 > CONECT 32 23 > CONECT 33 23 34 36 37 > CONECT 34 33 35 > CONECT 35 34 > CONECT 36 33 > CONECT 37 33 38 40 41 > CONECT 38 37 39 > CONECT 39 38 > CONECT 40 37 > CONECT 41 25 37 42 43 > CONECT 42 41 > CONECT 43 41 44 > CONECT 44 43 45 53 54 > CONECT 45 44 46 50 52 > CONECT 46 45 47 49 62 > CONECT 47 46 48 > CONECT 48 47 > CONECT 49 46 > CONECT 50 45 51 > CONECT 51 50 > CONECT 52 45 > CONECT 53 44 > CONECT 54 44 55 60 61 > CONECT 55 54 56 58 59 > CONECT 56 55 57 > CONECT 57 56 > CONECT 58 55 > CONECT 59 55 > CONECT 60 54 > CONECT 61 54 62 > CONECT 62 46 61 63 64 > CONECT 63 62 > CONECT 64 62 65 > CONECT 65 64 66 74 75 > CONECT 66 65 67 71 73 > CONECT 67 66 68 70 83 > CONECT 68 67 69 > CONECT 69 68 > CONECT 70 67 > CONECT 71 66 72 > CONECT 72 71 > CONECT 73 66 > CONECT 74 65 > CONECT 75 65 76 81 82 > CONECT 76 75 77 79 80 > CONECT 77 76 78 > CONECT 78 77 > CONECT 79 76 > CONECT 80 76 > CONECT 81 75 > CONECT 82 75 83 > CONECT 83 67 82 84 85 > CONECT 84 83 > CONECT 85 83 86 > CONECT 86 85 87 95 96 > CONECT 87 86 88 92 94 > CONECT 88 87 89 91 104 > CONECT 89 88 90 > CONECT 90 89 > CONECT 91 88 > CONECT 92 87 93 > CONECT 93 92 > CONECT 94 87 > CONECT 95 86 > CONECT 96 86 97 102 103 > CONECT 97 96 98 100 101 > CONECT 98 97 99 > CONECT 99 98 > CONECT 100 97 > CONECT 101 97 > CONECT 102 96 > CONECT 103 96 104 > CONECT 104 88 103 105 106 > CONECT 105 104 > CONECT 106 104 107 > CONECT 107 106 108 116 117 > CONECT 108 107 109 113 115 > CONECT 109 108 110 112 125 > CONECT 110 109 111 > CONECT 111 110 > CONECT 112 109 > CONECT 113 108 114 > CONECT 114 113 > CONECT 115 108 > CONECT 116 107 > CONECT 117 107 118 123 124 > CONECT 118 117 119 121 122 > CONECT 119 118 120 > CONECT 120 119 > CONECT 121 118 > CONECT 122 118 > CONECT 123 117 > CONECT 124 117 125 > CONECT 125 109 124 126 127 > CONECT 126 125 > CONECT 127 125 128 > CONECT 128 127 129 130 141 > CONECT 129 128 > CONECT 130 128 131 133 134 > CONECT 131 130 132 > CONECT 132 131 > CONECT 133 130 > CONECT 134 130 135 137 138 > CONECT 135 134 136 > CONECT 136 135 > CONECT 137 134 > CONECT 138 10 134 139 140 > CONECT 139 138 > CONECT 140 138 141 > CONECT 141 128 140 142 143 > CONECT 142 141 > CONECT 143 141 144 145 146 > CONECT 144 143 > CONECT 145 143 > CONECT 146 143 147 > CONECT 147 146 > -------------------------------------------------------------------------> > From owner-chemistry@ccl.net Wed Sep 17 16:53:01 2008 From: "Kalju Kahn kalju##chem.ucsb.edu" To: CCL Subject: CCL: extrapolation to CBS limit Message-Id: <-37765-080917164333-16912-CvfYaKjXDQt5ufTCxTAHLA---server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 17 Sep 2008 13:03:48 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju(!)chem.ucsb.edu] Dear Sujata, I do not claim to know the correct recipe but here are some of the ideas: 1) Extrapolate HF energy separately using T,Q,5 with exponential function E = E_inf + A*Exp[-B*X] where X is [3,4,5] and E is the corresponding SCF energy. Notice that you do not need DZ data point. You do not need to know the coefficients A and B; treat these as fit parameters. Notice that you can also solve this equation for E_inf in terms of energies; below is the Mathematica code and the result: Solve[{ETZ == Einf + A Exp[-3B], EQZ == Einf + A Exp[-4 B], E5Z == Einf + A Exp[-5B]}, Einf, {A, B}] Einf ->(-EQZ^2 + E5Z*ETZ)/(E5Z - 2*EQZ + ETZ) 2) Then extrapolate the correlation energy component from CCSD(T). I do not think that people agree on what is the most appropriate way to extrapolate CCSD(T) results (please feel free to add your suggestion here, anybody) but in general the convergence of correlation energy appears to follow a power law such as Ecorr = E_inf + A1*(X+c)^(-3) + A2*(X+c)^(-4) + A3*(X+c)^(-5) + ... The question is of course, where do you truncate? The first term with (-3) arises from slowly-converging singlet pairs and dominates. The second term (-4) may be a correction term from singlet pairs. The third term (-5) arises from rapidly-converging triplet pairs and seems to be important; it may also contain higher order corrections from singlets. So, if you have separate singlet and triplet pair energies at CCSD level, you can try Eccsd_singlets = E_inf + A1*(X+c)^(-3) using QZ, 5Z Eccsd_triplets = E_inf + A3*(X+c)^(-5) using QZ, 5Z The coefficient c depends on what your molecule is made of. If it has only H or He, c = 0; if it only has heavy atoms, c = 1. For a molecule with both heavy atoms and hydrogens, c = 0.5 is commonly used. Again, notice that after fixing c (to 0.5 in the case below), you can solve for E_inf. For singlet pairs: Einf -> (1331*E5Z - 729*EQZ)/602 For triplet pairs: Einf -> (161051*E5Z - 59049*EQZ)/102002 When I do not have singlet and triplet pairs, I like to use Ecorr = E_inf + A*(X+0.5)^(-3) + B*(X+0.5)^(-5) with energies at TZ, QZ, 5Z. This can be solved for E_inf: Solve[{ETZ == Einf + A/(3+1/2)^3+B/(3+1/2)^5,EQZ == Einf + A/(4+1/2)^3+B/(4+1/2)^5, E5Z == Einf + A/(5+1/2)^3+B/(5+1/2)^5}, Einf, {A,B} ] which yields: Einf -> (644204*E5Z - 531441*EQZ + 84035*ETZ)/196798 You can use the latter approach also for the (T) contribution in CCSD(T) when doing separate singlet/triplet pair extrapolation; I do not know if it is theoretically justified for (T) but it seems to work. Notice that you do not need to use DZ data. OK, let me rephrase: no not ever use DZ data when extrapolating correlation energies, unless you are trying to show someone how to get wrong results! Then you add the extrapolated SCF energy to the extrapolated correlation energy. You can compare the extrapolated results from cc-pVXZ and aug-cc-pVXZ series (these sometimes show quite different convergence patterns, I would be hard pressed to claim that aug-series is superior); if the results agree you are most likely OK. If it is a small system (less than three heavy atoms and elements HCNOF) you can carry out an explicitly correlated R12 calculation with a program such as DIRCCR12 as another check. P.S. There is good amount of literature about this, you may want to look up what Wim Klopper and Ed Valeev have published on this subject during the last decade. You may also want to take a look at out "Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets" for some ideas. Good luck, Kalju > > Sent to CCL by: "Sujata Guha" [sguha-*-tnstate.edu] > I have performed energy computations for a molecule at the CCSD(T)/cc-pVnZ > (where n=D,T,Q,5)and CCSD(T)/aug-cc-pVnZ (where n=D,T,Q,5) theory levels. > I'm trying to extrapolate the energies to the CBS limit for n=2-5 and am > not sure of the exact procedure. I'm trying to use the equation E(X) = > E(CBS) + Bexp-(X-1) + Cexp-(X-1)2. What values of B and C should I use and > how would I get an energy value for n=2-5? Sorry if the question sounds > basic - it is my first time to try this method of extrapolation. Any > information will be much appreciated. Thank you.> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Wed Sep 17 17:32:00 2008 From: "Susan R. Atlas susie||sapphire.phys.unm.edu" To: CCL Subject: CCL: Atomistix? Message-Id: <-37766-080917163204-14143-AA+PzJeLLvMgYVhXJU78SQ^^server.ccl.net> X-Original-From: "Susan R. Atlas" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Sep 2008 14:01:43 -0600 MIME-Version: 1.0 Sent to CCL by: "Susan R. Atlas" [susie.:.sapphire.phys.unm.edu] Hi, We have been using the commercial Atomistix atk and vnl codes (based on SIESTA and TRANSIESTA) for the past six months to calculate quantum transport properties (using a NEGF technique in DFT) for nanoscale (molecular electronic) applications, and the company website (atomistix.com) seems to have gone offline suddenly. Emails and phone calls are going unanswered. It has been over two weeks now, and that is longer than can be accounted for by a website crash, e.g. Google does not turn up any news about the company. Does anyone on this list have any knowledge of what is going on? If they are out of business suddenly, this will present a major research block for us and we would need to quickly find another code (commercial or freely available) with similar capabilities; any recommendations would be most appreciated. Thanks, Susan -- ------------------------------------------------------------------ Susan R. Atlas Research Associate Professor, Physics and Astronomy Director, Cancer Research and Treatment Center Shared Resource for Bioinformatics and Computational Biology Department of Physics & Astronomy MSC07 4220 p: 505.277.1509 1 University of New Mexico e: susie ~ sapphire.phys.unm.edu Albuquerque, NM 87131-0001 n: www.phys.unm.edu/CompMaterials From owner-chemistry@ccl.net Wed Sep 17 18:19:01 2008 From: "Mikael Johansson mpjohans%a%chem.au.dk" To: CCL Subject: CCL: extrapolation to CBS limit Message-Id: <-37767-080917181027-8622-bw1ZOBd3vWPkFlEC2pXSCg],[server.ccl.net> X-Original-From: Mikael Johansson Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Wed, 17 Sep 2008 23:11:59 +0200 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans^chem.au.dk] Hello Sujata! On Tue, 16 Sep 2008 "Sujata Guha sguha[]tnstate.edu" =20 wrote: > I have performed energy computations for a molecule at the =20 > CCSD(T)/cc-pVnZ (where n=3DD,T,Q,5)and CCSD(T)/aug-cc-pVnZ (where =20 > n=3DD,T,Q,5) theory levels. I'm trying to extrapolate the energies to =20 > the CBS limit for n=3D2-5 and am not sure of the exact procedure. I'm =20 > trying to use the equation E(X) =3D E(CBS) + Bexp-(X-1) + Cexp-(X-1)2. =20 > What values of B and C should I use and how would I get an energy =20 > value for n=3D2-5? At a quick glance, it looks like a three-point fitting formula, where =20 you set up a system of equations using three, most likely consecutive, =20 levels of basis sets for E(X), and then solve for E(CBS), B, and C. I =20 guess there's more info in the original reference for that =20 extrapolation scheme, perhaps with ball-park figures for B and/or C. For simplicity, I'd recommend the physically motivated two-point =20 formula by Halkier et co [1] (E(*) are the correlation energies): E(CBS) ~ E(XY) =3D (E(X)*X^3 - E(Y)*Y^3) / (X^3 - Y^3). Then you don't need any fitting at all, just insert the values of the =20 best basis sets, in your case X=3D4 and Y=3D5. You might want to =20 extrapolate the SCF energy separately. And as you have CCSD(T) results, why not extrapolate also toward the =20 FCI limit with Goodson's formula [2]! For an example of combining both extrapolations, see for example =20 http://dx.doi.org/10.1021/ct800182e Have a nice day, Mikael J. http://www.iki.fi/~mpjohans [1] Halkier, A.; Helgaker, T.; J=C3=B8rgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. "Basis-set convergence in correlated calculations on Ne, N2, and H2O." Chem. Phys. Lett. 1998, 286, 243=E2=80=93252. [2] Goodson, D. Z. "Extrapolating the coupled-cluster sequence toward the full configuration-interaction limit." J. Chem. Phys. 2002, 116, 6948=E2=80=936956. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Wed Sep 17 22:04:01 2008 From: "Jiten jiten(0)postech.ac.kr" To: CCL Subject: CCL: extrapolation to CBS limit Message-Id: <-37768-080917220002-10720-Ee3Eb2qxdqCSTljcR9HGDQ\a/server.ccl.net> X-Original-From: "Jiten" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="UTF-8"; reply-type=response Date: Thu, 18 Sep 2008 10:29:54 +0900 MIME-Version: 1.0 Sent to CCL by: "Jiten" [jiten[A]postech.ac.kr] Hello, You may also like to see the article on "Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes" auothors by Prof. Kim's group (J. Comput. Chem. 29, 1208-1221 (2008)) : http://csm.postech.ac.kr Sincerely, Jiten ----- Original Message ----- > From: "Mikael Johansson mpjohans%a%chem.au.dk" To: "SINGH, JITEN " Sent: Thursday, September 18, 2008 6:11 AM Subject: CCL: extrapolation to CBS limit Sent to CCL by: Mikael Johansson [mpjohans^chem.au.dk] Hello Sujata! On Tue, 16 Sep 2008 "Sujata Guha sguha[]tnstate.edu" wrote: > I have performed energy computations for a molecule at the > CCSD(T)/cc-pVnZ (where n=D,T,Q,5)and CCSD(T)/aug-cc-pVnZ (where > n=D,T,Q,5) theory levels. I'm trying to extrapolate the energies to the > CBS limit for n=2-5 and am not sure of the exact procedure. I'm trying > to use the equation E(X) = E(CBS) + Bexp-(X-1) + Cexp-(X-1)2. What values > of B and C should I use and how would I get an energy value for n=2-5? At a quick glance, it looks like a three-point fitting formula, where you set up a system of equations using three, most likely consecutive, levels of basis sets for E(X), and then solve for E(CBS), B, and C. I guess there's more info in the original reference for that extrapolation scheme, perhaps with ball-park figures for B and/or C. For simplicity, I'd recommend the physically motivated two-point formula by Halkier et co [1] (E(*) are the correlation energies): E(CBS) ~ E(XY) = (E(X)*X^3 - E(Y)*Y^3) / (X^3 - Y^3). Then you don't need any fitting at all, just insert the values of the best basis sets, in your case X=4 and Y=5. You might want to extrapolate the SCF energy separately. And as you have CCSD(T) results, why not extrapolate also toward the FCI limit with Goodson's formula [2]! For an example of combining both extrapolations, see for example http://dx.doi.org/10.1021/ct800182e Have a nice day, Mikael J. http://www.iki.fi/~mpjohans [1] Halkier, A.; Helgaker, T.; Jørgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. "Basis-set convergence in correlated calculations on Ne, N2, and H2O." Chem. Phys. Lett. 1998, 286, 243–252. [2] Goodson, D. Z. "Extrapolating the coupled-cluster sequence toward the full configuration-interaction limit." J. Chem. Phys. 2002, 116, 6948–6956. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -=his is automatically added to each message by the mailing script =http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt