From chemistry-request@server.ccl.net Wed Oct 30 04:36:29 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9U9aTX03306 for ; Wed, 30 Oct 2002 04:36:29 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 5773C56DDE4; Wed, 30 Oct 2002 10:36:27 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 58F0E56DDE1; Wed, 30 Oct 2002 10:36:25 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 30 Oct 02 10:36:25 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 30 Oct 02 10:36:15 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: jmmckel@attglobal.net, cc236@cornell.edu Date: Wed, 30 Oct 2002 10:36:15 +0100 Subject: CCL:Getting electronic spectrum info from Gaussian Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <38B0CC43EA5@virgil.ruc.dk> John McKelvey: > For organic systems the most reliable way in Gaussian is to optimize > the geometry with something like B3LYP/6-31G*, and then do ZINDO > with all single excitations. Use of semi empirical geometries > should be used with the utmost caution, particularly if molecules > are non-planar... they are "cheap," but.... I agree with John. - If you are willing to spend more CPU time, you may consider time-dependent density functional theory, f.inst. at the TD-B3LYP/6-31G* level. Juergen Fabian recently published a survey of electronic transitions predicted with TD-B3LYP, ZINDO, and PPP for a large number of sulfur-organic compounds - J. Fabian: "Electronic excitation of sulfur-organic compounds - performance of time-dependent density funcyional theory", Theor. Chem. Acc. 106, 199-217 (2001). Yours, Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Tue Oct 29 14:57:10 2002 Received: from adenine.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TJvAr26709 for ; Tue, 29 Oct 2002 14:57:10 -0500 Received: from localhost (socrates.cgl.ucsf.edu [128.218.27.3]) by adenine.cgl.ucsf.edu (8.12.3/8.12.3/GSC1.16) with ESMTP id g9TJv9Nf701179; Tue, 29 Oct 2002 11:57:10 -0800 (PST) Date: Tue, 29 Oct 2002 11:57:09 -0800 (PST) From: Pradipta Bandyopadhyay To: Patrik Johansson cc: chemistry@ccl.net Subject: Re: CCL:MC/sim-ann & Gamess! In-Reply-To: <3DB8F1FB.652C1ECF@fy.chalmers.se> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 25 Oct 2002, Patrik Johansson wrote: > Hi > > Happy for your answer, but I must ask again: how does one make the two > "fragments" anion and Na+ practically in the input - if one wants both > of them to be treated ab initio? One of them (the anion) I can of course > set in $DATA, but where do I put Na+ ? You have to define both in the $data group - if you want to treat both as ab initio. > > If I do a MC with all atoms in $DATA I partly loose the scope that the > position of Na+ should be varied the most and the anion only internally > relaxed somewhat or am I missing something in how the MC steps are > performed? Actually MC code in GAMESS is not yet that flexible. You have to change the code to do it. > > The computational time is not a big issue as the anion is rather small > (8-12 atoms) - and I've got plenty of CPU-hours :-) > > best regards > > /Patrik > > Pradipta Bandyopadhyay wrote: > > > > Hi, > > > > You can treat your system with full ab initio description without using > > EFP. The problem is that it is extremely expensive computationally. > > Moreover - only cartesian coordiantes are changed for ab initio part - > > which is very inefficient. If you can give the Monte Carlo moves using > > some internal coordiantes by changing the code it would be little better. > > Another possibility is that you can make a fragment from your large > > anionic molecule and then can treat the Na+ as ab initio and the large > > molecule as efrag. > > > > Hope this helps. > > > > Pradipta > > > > On Thu, 24 Oct 2002, Patrik Johansson wrote: > > > > > Dear CClers > > > > > > Has anyone tried to perform a MC/sim-ann calc within gamess using the > > > globop routine _and_ using two different ab initio parts (i.e. not using > > > efrag)? > > > > > > An example: to render starting positions for a Na+ ion around a large > > > anionic molecule which itself is allowed to relax and the Na-anion > > > interaction treated ab initio. > > > > > > Hints/examples anyone? > > > > > > I'll summarize the answers (if any) of course. > > > > > > best regards > > > /Patrik > > > -- > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Oct 30 05:26:21 2002 Received: from mserv7.dl.ac.uk ([148.79.80.138]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UAQKX04297 for ; Wed, 30 Oct 2002 05:26:20 -0500 X-DL-MFrom: X-DL-Connect: Received: from exchange06.dl.ac.uk (exchange06.dl.ac.uk [148.79.162.91]) by mserv7.dl.ac.uk (8.11.6/8.11.6/[ref postmaster@dl.ac.uk]) with ESMTP id g9UAQIr27618; Wed, 30 Oct 2002 10:26:18 GMT Received: by exchange06.dl.ac.uk with Internet Mail Service (5.5.2653.19) id <3WR95LSD>; Wed, 30 Oct 2002 10:23:48 -0000 Message-ID: From: "Sherwood, P (Paul)" To: chemistry@ccl.net Cc: "'David Feller'" , "'Carina Lansing'" , "Searle, BG (Barry)" Subject: EMSL basis library, european mirror available again Date: Wed, 30 Oct 2002 10:23:42 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" All, As some of you will know we maintain a mirror of the EMSL Gaussian basis set library developed by Dave Feller and colleagues at PNNL http://www.emsl.pnl.gov:2080/forms/basisform.html at Daresbury (UK). Due to server problems this has been unavailable for a while but it can now be found again on our new server at http://www.cse.clrc.ac.uk/qcg/basis Apologies to anyone who was inconvenienced. If you haven't used it recently the library now provides a large selection of basis sets in output formats suitable for a wide range of codes. regards, Paul Sherwood -- ================================================================= Dr Paul Sherwood, email: p.sherwood@daresbury.ac.uk CLRC Daresbury Lab, tel: +44-1925-603553 Warrington, fax: +44-1925-603634 WA4 4AD, UK. http: http://www.cse.clrc.ac.uk ================================================================= From chemistry-request@server.ccl.net Wed Oct 30 04:53:41 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9U9reX03678 for ; Wed, 30 Oct 2002 04:53:40 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 186pTM-0001mG-00; Wed, 30 Oct 2002 09:49:12 +0000 Date: Wed, 30 Oct 2002 09:49:12 +0000 (GMT) From: Szilveszter Juhos To: "Ruben E. Venegas" cc: chemistry@ccl.net Subject: Re: CCL:Stereo for PC In-Reply-To: <001001c27f88$d41c27d0$3601a8c0@TARGETEDMOLECULES.COM> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 29 Oct 2002, Ruben E. Venegas wrote: > What people are using for viewing structures in 3-D stereo on a PC (W2K > machine) ? My experience is that it is worth to learn crossed eyes or parallel eyes stereo. It is good to your eyes especially if you are using computers too much (like me). A very good stuff that works on both W2K and Unices is MOE (http://www.chemcomp.com/) that can do it. Unfortunatelly is is not free. You can have some stereo eyes intros from: http://www.vision3d.com/dots.html (I'd leart with its help in an http://www.vision3d.com afternoon) http://www.angelfire.com/ca/erker/freeview.html Tricks like being a bit far from the display at the first time and moving your head slowly to find the best matching can help. > in stereo mode. For example, I'd like to manually overlay two or more > molecules. That is a PITA. MOE also will superimpose things for you in no time much more better than you ever could do it by hand. And you do not even need stereo for that. The other (and free) tool is SwissPDB http://www.expasy.org/spdbv/ that will superpose PDBs. Sure there are other softwares that I am not aware of since I am rather challenged in using Windows ;) Szilva From chemistry-request@server.ccl.net Tue Oct 29 14:51:03 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TJp3r26504 for ; Tue, 29 Oct 2002 14:51:03 -0500 Received: from chem.iupui.edu ([134.68.137.128]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id OAA2386245; Tue, 29 Oct 2002 14:50:38 -0500 (EST) Message-ID: <3DBEF437.61E68D41@chem.iupui.edu> Date: Tue, 29 Oct 2002 14:48:57 -0600 From: "Boyd, D." X-Mailer: Mozilla 4.79C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: OSC CCL , CHMINF-L Subject: new book in comp chem Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Colleagues, Volume 18 of REVIEWS IN COMPUTATIONAL CHEMISTRY has been published. The chapters are: o Clustering methods and their uses o Scoring functions in drug discovery applications o Incorporating polarizability in computer simulations o Theoretical description of charge-transfer reactions o Linear free energy relationships o Development of computational chemistry in Germany The authors are: John M. Barnard, Hans-Joachim Boehm, Geoff M. Downs, George R. Famini, Dmitry V. Matyushov, Sigrid D. Peyerimhoff, Steven W. Rick, Martin Stahl, Steven J. Stuart, Gregory A. Voth, and Leland Y. Wilson. The bonus feature in Vol. 18 is an appendix describing the employment picture for computational chemists. Copies of this and earlier volumes may be obtained for inspection from Wiley (www.wiley.com). Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Wed Oct 30 12:01:57 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UH1uf13431 for ; Wed, 30 Oct 2002 12:01:56 -0500 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-025 #30546) id <01KOA9P87B4G0010NE@unisi.it> for chemistry@ccl.net; Wed, 30 Oct 2002 18:01:55 +0100 (MET) Received: from unisi.it (ccmaol3.chim.unisi.it [192.167.123.208]) by unisi.it (PMDF V6.0-025 #30546) with ESMTPA id <01KOA9P7EWAE0014U0@unisi.it> for chemistry@ccl.net; Wed, 30 Oct 2002 18:01:54 +0100 (MET) Date: Wed, 30 Oct 2002 17:59:53 +0100 From: "Nicolas Ferre'" Subject: Angular momentum Sender: ferre@unisi.it To: chemistry@ccl.net Message-id: <3DC01009.87E986B9@unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.61i [en_US] (X11; I; AIX 4.3) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: fr, en Dear CCL, I'd like to find some general references (reviews, books ...) about the theory/calculation of electronic orbital angular momentum in the case of a molecular system (i.e. beside the atom and the diatomic molecule cases). In particular, what are the theoretical problems (e.g. if an electron is described with a molecular orbital, what is the origin in space of the corresponding angular momentum) and what are the solutions proposed. Thanks for your help. Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre@unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Oct 30 12:23:56 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UHNuf14112 for ; Wed, 30 Oct 2002 12:23:56 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id MAA12092 for ; Wed, 30 Oct 2002 12:23:51 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DC015A8.EB63F78A@cornell.edu> Date: Wed, 30 Oct 2002 12:23:52 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.16smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian98 frequency calculations using FREQ keyword Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all -- I have a question about the output from using the FREQ keyword. I first optimized the structure with OPT and then used FREQ to calculate the normal modes. In the output, where are the normal coordinate vectors and/or the Hessian matrix? I've found something that looks like it is a Hessian matrix -- it's called the full mass weighted force constant matrix as follows: My question is 1) what are the elements of the force constant matrix. Is it the "Frc consts" or is it the elements below that under the X Y Z heading for individual atoms? Are they the same thing, but one is in a vectorized form and the other in component form? 2) why are the force constants only accurate or shown to 2 sig figs? Where or how can I get more digits out? Full mass-weighted force constant matrix: Low frequencies --- -5.1861 -1.6047 -1.2255 -0.0066 0.0480 1.8398 Low frequencies --- 20.1222 22.2472 32.0298 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 ?A ?A ?A Frequencies -- 20.1068 22.2471 32.0298 Red. masses -- 12.0000 12.0000 12.0000 Frc consts -- 0.0029 0.0035 0.0073 IR Inten -- 0.0000 0.0091 0.0030 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 Atom AN X Y Z X Y Z X Y Z 1 6 0.01 -0.03 0.09 0.03 0.02 0.05 0.06 0.09 0.00 2 6 0.01 -0.02 0.07 0.02 0.01 0.08 0.02 0.11 0.00 3 6 0.00 0.00 0.11 0.00 0.00 0.03 0.08 0.08 0.00 4 6 0.03 -0.06 0.08 0.05 0.03 0.03 0.06 0.07 0.00 5 6 -0.01 0.02 0.07 -0.02 -0.01 0.08 0.02 0.11 0.00 6 6 -0.01 0.03 0.09 -0.03 -0.02 0.05 0.06 0.09 0.00 7 6 0.00 0.00 0.11 0.00 0.00 -0.01 0.09 0.05 0.00 8 6 0.03 -0.05 0.09 0.05 0.03 -0.01 0.08 0.04 0.00 9 6 0.04 -0.07 0.05 0.07 0.04 0.04 0.02 0.06 0.00 10 6 0.02 -0.03 0.04 0.03 0.02 0.09 -0.01 0.10 0.00 11 6 -0.03 0.06 0.08 -0.05 -0.03 0.03 0.06 0.07 0.00 Thank you! Connie From chemistry-request@server.ccl.net Wed Oct 30 13:44:05 2002 Received: from ALPHA1.FANDM.EDU ([155.68.1.87]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UIi5f16084 for ; Wed, 30 Oct 2002 13:44:05 -0500 Received: from [155.68.51.192] by email.fandm.edu (PMDF V6.1 #39478) with ESMTPA id <01KOA0PGWJ9295UFXS@email.fandm.edu> for chemistry@ccl.net; Wed, 30 Oct 2002 13:44:02 -0400 (EDT) Date: Wed, 30 Oct 2002 13:43:52 -0500 From: "Ronald L. Musselman" Subject: resonance integrals in HyperChem's ZINDO To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Hello ZINDO users: I'm having some trouble ferreting out the details regarding beta values (resonance integrals), etc. in ZINDO, especially the implementation from HypeCube, with regard to UV-vis spectral calculations. The manual (CC, p307) leaves a lot unstated. I'd greatly appreciate being directed to a good source that deals with these specifics, or even a short direct answer if possible. My understanding of the relationship among resonance and overlap integrals is that, beta_uv = beta_AB * S_uv where u refers to MO_u on atom A, v refers to MO_v on an adjacent atom B, beta_uv is the resonance integral, beta_AB is the overlap weighting factor, and S_uv is the overlap integral. Is this correct? Assuming the above is OK, I understand that the overlap weighting factors in HyperChem7 are intended to provide better results when doing spectroscopic calculations. Thus, the factors should be 1.0 when using ZINDO/1 and not 1.0 when using ZINDO/S. My question, then is, if the weighting factor adjusts the S_uv for a better beta_uv for spectra, why does it appear that there are different values of beta_uv for ZINDO/1 and ZINDO/S? Is this not double adjusting? Perhaps a more fundamental question is, are the beta s,p, and d values listed in files zindo1_1.abd and zindoS_1.abd the same as beta_uv in the equation above? Also, there appear to not be any weighting factors for d orbitals; is this true? Thanks to those who have read all the way down to here! Sincerely, Ron Musselman -- * Reflections from the desk of: * ___ * * / * * ________*_________________________ |_________________________________| | Ronald L. Musselman | | Professor of Chemistry | | Franklin and Marshall College | | Lancaster, PA 17604 USA | | Ronald.Musselman@fandm.edu | | (717) 291-3802 Fax 291-4343 | |_______________________________| From chemistry-request@server.ccl.net Wed Oct 30 13:56:55 2002 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UIutf16511 for ; Wed, 30 Oct 2002 13:56:55 -0500 Received: from pc1 (ntred1 [128.227.192.113]) by qtp.ufl.edu (8.9.1a/8.9.1/deumens) with SMTP id NAA16595; Wed, 30 Oct 2002 13:56:54 -0500 (EST) Message-ID: <038201c28047$5426fdb0$71c0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Connie Chang" Cc: "CCL - all" References: <3DC015A8.EB63F78A@cornell.edu> Subject: Re: CCL:Gaussian98 frequency calculations using FREQ keyword Date: Wed, 30 Oct 2002 14:05:35 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Connie, the shown piece of the output contains the harmonic frequencies, other spectroscopic data and then the vibrational modes in cartesian coordinates (with respect to the "Standard Orientation"). You can increase the number of decimals with # ... freq(hpfreq) You can tune the completeness of the output of the links with IOPs: # ... IOP(x/y=z) with x,y,z integers They are documented in the "programmers reference" and maybe in the header of the link1 source code (just read it with more, less, or some editor). Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2319 NPB #92, P.O.Box 118435 Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Wed Oct 30 14:42:43 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UJghf17621 for ; Wed, 30 Oct 2002 14:42:43 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id OAA27349 for ; Wed, 30 Oct 2002 14:42:43 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DC03633.B840DC48@cornell.edu> Date: Wed, 30 Oct 2002 14:42:43 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.16smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Another Gaussian98 question RE Freq and Hessian matrix Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all -- I'm sorry to be flooding your mailboxes with my silly questions, but I've discovered another sticking point that I'm not sure how to solve... I am looking for the Hessian matrix for the molecule I am working with. The dimensions of the Hessian should be (# of atoms * 3) x (# of atoms *3) but I've just discovered that Gaussian only gives {(# of atoms *3) - 6} normal modes. The 6 missing are the low-lying translational/rotational modes I am guessing. But I need the full Hessian for the calculation I am considering. Is the full Hessian stored elsewhere? How can I access it? Thanks, Connie From chemistry-request@server.ccl.net Wed Oct 30 09:10:15 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UEAEf08786 for ; Wed, 30 Oct 2002 09:10:15 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA26436; Wed, 30 Oct 2002 09:10:10 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3DBFE842.B4D8D62@cornell.edu> Date: Wed, 30 Oct 2002 09:10:10 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Aaron Deskins CC: CCL Subject: Re: CCL:damped molecular dynamics References: <3DBEE809.F4D7E0C5@ecn.purdue.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In dynamics with friction and stochastic terms there is the tendency to mask problems in the underlying trajectory integration/dynamics. I believe the step size should be chosen so that zero-friction dynamics is stable for long time ... that way you know the underlying dynamics is good. Usually for dynamics, you would choose a stepsize of 1 or 2 fsec when hydrogen atoms are present. With a unified atom model or bond-length constraints you can go larger. The step size you need must be smaller than a typical oscillation period for any coordinate. Oscillation period depends upon both the stiffness of the spring and the effective mass of the atom or body. You could then turn up the friction a little to give you what you want. I assume you are using it as a sort of simulated annealing? I would love to know how others choose good friction terms for Langevin type simulations. Perhaps others will comment. Richard Gillilan MacCHESS, Cornell > 2) What are good strategies to decide the friction coefficient and time > step? I noticed that if the time step is too large, the kinetic > instabilities are common. > > thanks for any help. > > Aaron Deskins > Purdue University > From chemistry-request@server.ccl.net Wed Oct 30 11:56:42 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UGugf13199 for ; Wed, 30 Oct 2002 11:56:42 -0500 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-025 #30546) id <01KOA9IPXFXC0014V6@unisi.it> for CHEMISTRY@ccl.net; Wed, 30 Oct 2002 17:56:40 +0100 (MET) Received: from unisi.it (sgio2.ctf.unisi.it [172.16.3.81]) by unisi.it (PMDF V6.0-025 #30546) with ESMTPA id <01KOA9IP97S80014U0@unisi.it> for CHEMISTRY@ccl.net; Wed, 30 Oct 2002 17:56:39 +0100 (MET) Date: Wed, 30 Oct 2002 17:55:55 -0800 From: Stefano Forli Subject: About exporting to 3D formats Sender: stefano@unisi.it To: CHEMISTRY@ccl.net Message-id: <3DC08DAB.627F49FD@unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=UTF-7 Content-transfer-encoding: 7BIT X-Accept-Language: en Previously I asked for some softwares able to export molecular structures, expecially with secondary structures representations (ribbons, cartoons, and so on...). I'm very interested to find a way to import structure data in 3D packages as Lightwave3D to generate movies, but all the programs I tested work well with POV-Ray or VRML format. I found the free program VMD at link http://www.ks.uiuc.edu/Research/vmd/ that can generate input files for different rendering suites: Rayshade, Renderman, Radiance, Lightwave 3D... I hope it can be useful. Best regards. -- *********************************** Forli Stefano Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 *********************************** From chemistry-request@server.ccl.net Wed Oct 30 08:59:01 2002 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UDx1f08456 for ; Wed, 30 Oct 2002 08:59:01 -0500 Received: from attglobal.net (slip-12-64-91-173.mis.prserv.net[12.64.91.173]) by prserv.net (out4) with SMTP id <2002103013590020402hb81qe>; Wed, 30 Oct 2002 13:59:00 +0000 Message-ID: <3DBF9FA4.8D06D050@attglobal.net> Date: Wed, 30 Oct 2002 09:00:20 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: spanget@ruc.dk CC: cc236@cornell.edu, chemistry@ccl.net Subject: Re: CCL:Getting electronic spectrum info from Gaussian References: <38B0CC43EA5@virgil.ruc.dk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit OOPS, I left out P.J. Hay and Richard L Martin John Jens Spanget-Larsen wrote: > John McKelvey: > > > For organic systems the most reliable way in Gaussian is to optimize > > the geometry with something like B3LYP/6-31G*, and then do ZINDO > > with all single excitations. Use of semi empirical geometries > > should be used with the utmost caution, particularly if molecules > > are non-planar... they are "cheap," but.... > > I agree with John. - If you are willing to spend more CPU time, you > may consider time-dependent density functional theory, f.inst. at > the TD-B3LYP/6-31G* level. Juergen Fabian recently published a survey > of electronic transitions predicted with TD-B3LYP, ZINDO, and PPP for > a large number of sulfur-organic compounds - > > J. Fabian: "Electronic excitation of sulfur-organic compounds - > performance of time-dependent density funcyional theory", Theor. > Chem. Acc. 106, 199-217 (2001). > > Yours, Jens >--< > > NB! Please note new mail address: > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget@ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Oct 30 08:57:33 2002 Received: from prserv.net ([32.97.166.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UDvXf08423 for ; Wed, 30 Oct 2002 08:57:33 -0500 Received: from attglobal.net (slip-12-64-91-173.mis.prserv.net[12.64.91.173]) by prserv.net (out2) with SMTP id <2002103013573120202cqqr7e>; Wed, 30 Oct 2002 13:57:32 +0000 Message-ID: <3DBF9F4B.FD493212@attglobal.net> Date: Wed, 30 Oct 2002 08:58:51 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: spanget@ruc.dk CC: cc236@cornell.edu, chemistry@ccl.net Subject: Re: CCL:Getting electronic spectrum info from Gaussian References: <38B0CC43EA5@virgil.ruc.dk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A further comment: If you want to hear the latest on computing spectra usung the latest ab-initio based methods, namely TDDFT, and related methods, you are urged to attend the symposium on this at the New Orleans ACS meeting March 23-27, 2003. Geometries of excited states using TDDFT will also be discussed. Speakers: E. J. Baerands Mark Casida Ken Wiberg John Jean Filipp Furche Tom Ziegler Jochen Autschbach Martin Head-Gordon Frank Neese Stefan Grimme Kieron Burke Mel Levy Weito Yang Serg Tretiak Gary Trucks Rod Bartlett Regards, John McKelvey Kieron Burke Jens Spanget-Larsen wrote: > John McKelvey: > > > For organic systems the most reliable way in Gaussian is to optimize > > the geometry with something like B3LYP/6-31G*, and then do ZINDO > > with all single excitations. Use of semi empirical geometries > > should be used with the utmost caution, particularly if molecules > > are non-planar... they are "cheap," but.... > > I agree with John. - If you are willing to spend more CPU time, you > may consider time-dependent density functional theory, f.inst. at > the TD-B3LYP/6-31G* level. Juergen Fabian recently published a survey > of electronic transitions predicted with TD-B3LYP, ZINDO, and PPP for > a large number of sulfur-organic compounds - > > J. Fabian: "Electronic excitation of sulfur-organic compounds - > performance of time-dependent density funcyional theory", Theor. > Chem. Acc. 106, 199-217 (2001). > > Yours, Jens >--< > > NB! Please note new mail address: > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget@ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Oct 30 15:40:17 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UKeGf19114 for ; Wed, 30 Oct 2002 15:40:16 -0500 Received: from localhost (sundius@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id WAA00218; Wed, 30 Oct 2002 22:40:05 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: sundius owned process doing -bs Date: Wed, 30 Oct 2002 22:40:05 +0200 (EET) From: Tom Sundius X-Sender: To: Connie Chang cc: Subject: Re: CCL:Gaussian98 frequency calculations using FREQ keyword In-Reply-To: <3DC015A8.EB63F78A@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 30 Oct 2002, Connie Chang wrote: > Hi all -- > > I have a question about the output from using the FREQ keyword. I first > optimized the structure with OPT and then used FREQ to calculate the > normal modes. > > In the output, where are the normal coordinate vectors and/or the > Hessian matrix? I've found something that looks like it is a Hessian > matrix -- it's called the full mass weighted force constant matrix as > follows: > Hi Connie, If you want a more complete output, you should add p on the route card: #p ... After the list of frequencies and eigenvectors you will then get the Hessian listed both in terms of internal coordinates and in terms of cartesian coordinates (the units are, however, not the same as those used in most NCA programs). Of these, the matrix expressed in cartesian coordinates is the most useful one. The archive part of the output (at the end of the log file) also contains the Hessian in cartesian coordinates. If you look at it closely, you can find a line that looks like this: ),SGV(H2)]\NImag=0\\0.05135282,0.,0.00000017,0.01887735,0.,0.56374193, (this was from a MP2 calculation on the water molecule) NImag=0 means there are no imaginary frequencies. After the double backslash you have the Hessian in cartesian coordinates. The order of the matrix elements is the same as in the output you get with the p option (a triangular matrix). Best regards, Tom Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 +++ for we know in part, and we prophecy in part +++ From chemistry-request@server.ccl.net Wed Oct 30 16:50:18 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9ULoHf21694 for ; Wed, 30 Oct 2002 16:50:18 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Wed, 30 Oct 2002 16:50:14 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Wed, 30 Oct 2002 16:49:50 -0500 From: "Peter Gannett" To: Subject: calculate tau (out of plane displacement) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi I'm trying to calculate tau, the out of plane displacement for a central atom to which three others are attached (eg for I-J-K-L, K is the central atom, I, J, L are attached), assuming you know all bond lengths between K and the attached atoms and all angles (I-K-L, etc). I have made a weak attempt at coming up with this but since this value is often reported (without reference as to how it was determined/calc) I was hoping that someone had the necessary equations to figure this out. Thanks. Pete From chemistry-request@server.ccl.net Wed Oct 30 16:26:56 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9ULQtf20831 for ; Wed, 30 Oct 2002 16:26:56 -0500 Received: from localhost (sundius@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id XAA19047; Wed, 30 Oct 2002 23:26:54 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: sundius owned process doing -bs Date: Wed, 30 Oct 2002 23:26:53 +0200 (EET) From: Tom Sundius X-Sender: To: Connie Chang cc: Subject: Re: CCL:Another Gaussian98 question RE Freq and Hessian matrix In-Reply-To: <3DC03633.B840DC48@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 30 Oct 2002, Connie Chang wrote: > Hi all -- > > I'm sorry to be flooding your mailboxes with my silly questions, but > I've discovered another sticking point that I'm not sure how to solve... > > I am looking for the Hessian matrix for the molecule I am working with. > The dimensions of the Hessian should be (# of atoms * 3) x (# of atoms > *3) but I've just discovered that Gaussian only gives > {(# of atoms *3) - 6} normal modes. The 6 missing are the low-lying > translational/rotational modes I am guessing. But I need the full > Hessian for the calculation I am considering. Is the full Hessian > stored elsewhere? How can I access it? I do not think so. For a molecule with 7 atoms, for instance, the number of Hessian elements is (3*7)^2 = 441, but if you store the lower or upper triangle, you get 3*7(3*7+1)/2 = 231, which is what I found in the archive part of the Gaussian output. You are now thinking of the number of normal modes which is something else. Greetings, Tom Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 +++ for we know in part, and we prophecy in part +++ From chemistry-request@server.ccl.net Wed Oct 30 18:01:06 2002 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9UN15f25343 for ; Wed, 30 Oct 2002 18:01:05 -0500 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (/8.10.1) with ESMTP id g9UN154W005563; Wed, 30 Oct 2002 18:01:06 -0500 (EST) Date: Wed, 30 Oct 2002 17:47:22 -0500 From: Rick Venable To: Richard Gillilan cc: Aaron Deskins , CCL Subject: Re: CCL:damped molecular dynamics In-Reply-To: <3DBFE842.B4D8D62@cornell.edu> Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII First, a citation-- --------------- LONCHARICH RJ, BROOKS BR, PASTOR RW LANGEVIN DYNAMICS OF PEPTIDES - THE FRICTIONAL DEPENDENCE OF ISOMERIZATION RATES OF N-ACETYLALANYL-N'-METHYLAMIDE BIOPOLYMERS 32 (5): 523-535 MAY 1992 Abstract: The rate constant for the transition between the equatorial and axial conformations of N-acetylalanyl-N'-methylamide has been determined from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is maximum at collision frequency gamma = 2 ps-1, shows diffusive character for gamma greater-than-or-equal-to 10 ps-1, but does not approach zero even at gamma = 0.01 ps-1. This behavior differs from that found for a one-dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., gamma almost-equal-to 2 ps-1). This method is expected to be more efficient than either molecular dynamics in vacuo (which corresponds to LD with gamma = 0) or molecular dynamics in solvent (where dynamics is largely diffusive). --------------- In essence, low friction (gamma = 2 ps-1) can accelerate barrier crossing rates, and improve sampling of phase space. For a simulated annealing or other sampling strategy, where you are not interested in timescales of motions, I highly recommend using low friction. For reference, the collision frequency of water is ca. 50 ps-1. On Wed, 30 Oct 2002, Richard Gillilan wrote: > In dynamics with friction and stochastic terms there is the > tendency to mask problems in the underlying trajectory > integration/dynamics. I believe the step size should be > chosen so that zero-friction dynamics is stable for long > time ... that way you know the underlying dynamics is good. > Usually for dynamics, you would choose a stepsize of 1 or 2 > fsec when hydrogen atoms are present. With a unified atom model > or bond-length constraints you can go larger. The step size you > need must be smaller than a typical oscillation period for any > coordinate. Oscillation period depends upon both the stiffness > of the spring and the effective mass of the atom or body. > > You could then turn up the friction a little to give you > what you want. I assume you are using it as a sort of > simulated annealing? > > I would love to know how others choose good friction terms for > Langevin type simulations. Perhaps others will comment. ------------------- > > 2) What are good strategies to decide the friction coefficient and time > > step? I noticed that if the time step is too large, the kinetic > > instabilities are common. > > > > thanks for any help. > > > > Aaron Deskins > > Purdue University =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=