From chemistry-request@ccl.net Fri Mar 13 06:09:30 1992 Date: Fri, 13 Mar 92 10:37:03 +0100 From: martin@biokth.sunet.SE (Martin Norin, Dept. Biochem., Royal Inst. Subject: MOPAC -reduced masses.. To: "chemistry@ccl.net"@kth.sunet.SE Status: R Dear Netters, When doing force calculations with MOPAC one gets the reduced masses of the vibrations. To my knowledge the reduced mass for a diatomic is m1*m2/(m1+m2) However MOPAC reports a reduced mass of 0.65 and 0.59 for HCL and HI. Shouldn't they be close to 1 or is it some more complications to the reported masses ? Greetings, /martin ************************************************************************ Martin Norin tel: +46-8-790 7512 Dept. Biochem fax: +46-8-723 1890 KTH e-mail: martin@physchem.kth.se 100 44 Stockholm Sweden ************************************************************************ DISCLAIMER: There is a theory that says that if anyone ever understands the laws of the Universe and why it exists it will immediately be replaced by something even more incomprehensible. Another theory says that this have already happened. /Freely after Douglas Adams. From jkl@ccl.net Fri Mar 13 09:11:34 1992 Date: Fri, 13 Mar 1992 09:11:30 -0500 From: jkl@ccl.net To: chemistry@ccl.net Subject: Re: vibration-rotation interaction constant, alpha Status: R Forwarding to the list: ---------- Begin Forwarded Message ---------- Date: Fri, 13 Mar 92 15:54:28 EST To: chemistry-request@ccl.net From: inm502@huxley.anu.edu.au Subject: vibration-rotation interaction constant, alpha I am looking for programs that allow me to calculate vibration-rotation interaction constants for linear triatomic. Any hints will be appreciated. Ida ============================================================================ Today your life may seem unbearable, but this time next year, you'll look back and realise that it was a picnic. ---------------------------------------------------------------------------- Research School of Chemistry, Australian National University, GPO Box 4, ACT 2601, Australia. Telephone: 06-2493509(w), 06-249665(h) ============================================================================ ----------- End Forwarded Message ----------- From rs0thp@rohmhaas.com Fri Mar 13 10:25:03 1992 From: rs0thp@rohmhaas.com (Dr. Tom Pierce) Subject: Re: Time step in MD To: jkl@ccl.net Date: Fri, 13 Mar 92 10:17:52 EST Status: R Jan Writes:> > The discussion on the cutoff distances and time steps is very stimulating. > However, I do not understand something here. > The time step chosen in Molecular Dynamics is for me a purely mathematical > parameter affecting the precision of integration, but not the physics of the > simulated system. If we had computers with infinite precision and infinite > speed, we should use the small integration step (e.g., 1.0E-20 s). But > our machines have final floating point precision and we cannot go too small > or the truncation errors will add up substantially. Also the machines of > today are slow, and we would not get results in our lifetime. > On the other hand, choosing the integration step too large would result in > errors in integration (like numerically integrating the sin function > with a step of 180 degrees) and would produce wrong trajectories. > For me, time step in MD is mathematics, not physics, like choosing > the grid size in numeric Hartree-Fock atomic calculations: > the smaller the better, and the smaller is much below Heisenberg principle. >... > Jan Labanowski > Ohio Supercomputer Center > jkl@ccl.net There is some physics here. I will speak from my experience with Enzyme Kinetics and Stiff ODEs with fast and slow components.In enzyme kinetics I had to make the stepsize(timestep) to be less than the change in concentration of the enzyme catalyst change over the timestep. This was because if the timesteps were too big, I would 'overlook' the loss or regeneration of enzyme. This led to violation of mass balance equations. Similarly in MD we have to capture the effects that act over a distance within a certain timestep. If the magnitude of the effect (force) is less than the accuracy of the computer then we cannot 'use' a timestep that small, and if the error involved in ignoring that magnitude does not dampout back to the 'correct' solution, then we cannot solve the problem because the physics requires a solution more accurate than the computer we are using.(Straightforward examples are shown in "Computer Methods for Mathematical Computations' by Forsythe et al pp 112 - called truncation error and roundoff error.)Usually the equations are 'stable' and small perturbations damp-out back to the desired solution. However, if the forces have a large effect during the timestep then the solution can be 'kicked' into a different curve - and we would violate physics laws like creating mass or energy. With cutoffs we are assuming that the error imposed by ignoring the change in forces beyond the cutoff is small and does not grow as the numerical solution progresses. To me this means that only columb forces need to be considered for large cutoffs. If the forces act over large distances AND the magnitude of a change in forces over the timestep is significant, then the problem has to be dealt with BECAUSE of the physics of the simulation. -- -------------------------------------------------------------------- Sincerely, Thomas Pierce Computer Applications Research | rs0thp@rohmhaas.com Internet Bldg 64C, Rohm and Haas Co. | rs0thp@rohvm1 Bitnet P.O. Box 219 | (215)-785-8989 Voice Bristol, PA 19007 | (215)-781-4204 Fax Official Disclaimer: "The opinions expressed are those of the writer and not the Rohm and Haas Company." From chemistry-request@ccl.net Fri Mar 13 12:15:31 1992 Date: Fri, 13 Mar 92 10:26:14 EST From: Michael Weiss Subject: cutoffs and the speed of light To: chemistry@ccl.net Status: R I too am puzzled by the discussion about cutoffs and the speed of light. The original post seemed to imply that the electrostatic force felt by charge B due to charge A at time t should be corrected by the delay effect, so B feels the force at time t+r/c, where r is the separation between A and B. But the formula for the electric field already contains an "extrapolation term", so that if, hypothetically, A were moving at uniform velocity, then the force on B could be calculated using the current position of A (current in B's rest frame). (See Feynman's Lectures, equation 28.3) Of course there is the radiation term, and the magnetic force, and the difference between a linear extrapolation and the actual non-uniform motion of the particles. Are these significant for the velocities and accelerations typical for MD simulations? Am I missing something? From chemistry-request@ccl.net Fri Mar 13 19:13:09 1992 Date: Fri, 13 Mar 1992 17:37 EST From: "DOUGLAS A. SMITH" Subject: coupled cluster methods question To: chemistry@ccl.net Status: R I have been reading up on coupled cluster methods, particularly using single, double and triple excitation. It appears to be an excellent although expensive method for open shell systems. 1. Is it the best method currently available for open shell molecules? 2. How will CCD or CCSD(T) perform on closed shell molecules? I have several systems to compare, and I would like to use a single consistant method for my calculations. 3. Is there a minimum basis set that should be used for CCD or CCSD(T)? Is there a practical limit to the size of a molecule which can be looked at using these methods? I know that this is a very loosely defined and open-ended question, but let me hear your opinions. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email fax0236@uoft02.utoledo.edu From jkl@ccl.net Fri Mar 13 19:50:54 1992 To: chemistry@ccl.net Subject: Summary of BIG AB INITIO Date: Fri, 13 Mar 92 19:50:37 EST From: jkl@ccl.net Status: R And this is a summary of responses on BIG AB INITIO. Sorry for deletions, but it is big even without them. Jan jkl@ccl.net ================================================== My original(?) question: Subject: The future of ab initio Date: Tue, 03 Mar 92 14:50:56 EST From: jkl@ccl.net Dear netters, We, in the Ohio Supercomputer Center, are trying to predict the trends and needs in computational chemistry of the (near) future. And as usual, there are more questions than answers. I have a big favo(u)r to ask. Please, answer me the following question: What would you do if you could ROUTINELY perform ab initio calculations (let say at the level of HF or HF/MP2) with 500 contracted basis functions? What kind of projects and applications would you run? Can you think about any commercial R & D applications where ab initio methods are important at this level. Thank you very much in advance. Mail it to me (jkl@ccl.net), and I will summarize the responses. Jan Labanowski ==================================== >From GERSON@dfwvm04.vnet.ibm.com Tue Mar 3 16:43:35 1992 Date: Tue, 3 Mar 92 15:41:41 CST From: "Dr. Dennis Gerson" Subject: Abinitio Futures At IBM (even those of us in technical marketing support do applied research in joint projects with IBM Research Division) we are looking at computational tools to simulate "real world" behaviour of polymers under processing conditions. The polymers are used as adhesives, photoresits or media sub- strates (like CDs, floppys or tape). As such we need to calculate properties such as thermal expansion coefficient, 2nd and 3rd order polarizabilities, UV spectra, fugacity. Most of our calculations are done at the MP2 level using HF hamiltonians except when we are looking at excited states. Most UV spectra are calculated using CNDO/S as a first approximation. Most of the systems are 80-150 heavy atoms and require a 6-31G*basis for properties and a 3-21G* for geometry. Our dynamics and mechanics are done using parameters developed from abinitio into the CHARMm and Discover force fields. I hope this helps....Regards, Dennis Gerson ==================================== >From cushing@smoked.cse.ogi.edu Tue Mar 3 20:21:03 1992 From: Judy Bayard Cushing Subject: Re: The future of ab initio ...as a computer scientist just beginning to study ab initio codes, and as a database specialist, i would guess that anyone who routinely performed lots of ab initio calculatins of the level you specified would want to interface with a database system to hold his/her results (at a minimum) and to peruse other's previous (successful) runs.... (--deleted--) --judy cushing oregon graduate institute. ==================================== >From d3e353@minerva.pnl.gov Tue Mar 3 20:26:53 1992 Date: Tue, 03 Mar 92 17:23:17 -0800 From: d3e353@minerva.pnl.gov Subject: Re: The future of ab initio Jan, We are rather close to putting in place some of the large scale computing capabilities that you describe, here at Pacific Northwest Laboratory. Massively parallel versions of direct SCF and direct MP2 are being finished up and tested by members of our Molecular Science Software Group and their collaborators. Our parallel machine is the 512 processor Intel Touchstone Delta Computer located at Caltech (and the Intel iPSC/860 at PNL), but these codes can run on other distributed memory or shared memory machines with few modifications (if any). Our present code development work specifically targets the 500-1000 basis function range on massively parallel machines. At PNL, we need to be able to do calculations of this size (and larger) to model molecular processes in the environment, dealing with environmental restoration and waste remediation. Most of this chemistry is in solution phase, and requires an array of computational methods to study it. Quantum chemistry is just one of the required approaches. For example, we also pursue large scale molecular dynamics computations for enzyme redesign, and have developed a new massively parallel code for large biopolymer simulations in the 20,000-100,000 atom range, with classical force fields. Another prototype nearing completion is a massively parallel Local Density Functional method for periodic systems. Ray Bair Group Leader, Molecular Science Software Molecular Science Research Center Pacific Northwest Laboratory d3e353@pnlg.pnl.gov ======================================= Date: Tue, 3 Mar 92 18:38:13 EST From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: The future of ab initio (--deleted--) HF/6-31G* on C30H62 with no symmetry (574 basis functions) takes well under a day in Gaussian 90 on an inexpensive workstation (RS/6000 model 530). Shouldn't that question be "What applications do you do now that such calculations have been possible for a couple of years?" Michael Frisch Gaussian, Inc. ========================================== Date: Tue, 3 Mar 92 22:31:36 -0500 From: neal@vision.poly-eng.uakron.edu (Neal Neuburger) (--deleted--) Perhaps, determining the spectral properties of UV absorbers in/for polymer additives. Or, determining the spectral properties, of organic pigments. Neal Neuburger ========================================= Date: Tue, 3 Mar 1992 22:41 EST From: KANTERS@urvax.urich.edu Subject: Re: The future of ab initio Hello Jan, I just saw you message regarding the future of ab inition calculations. I am very new in all this. My background is mainly in Inorganic Chemistry, more specifically gold-phosphine clusters. I did some EHMO calculations on these type of compounds to rationalize structural changes upon chemical mo- dification. For a lot of this kind of things I find extended Huckel satis- factorily. At the moment I am collaborating with another Inorganic Chemist who works on Re-di-imine complexes. For this research we are interested in more quantita- tive calculations in order to be able to predict what modifications in the ligand system will give us the desired UV/VIS absorbtions. With that in mind we want to run Argus (by Mark Thompson, when he releases it) or ZINDO on the computing facilities we have here at Richmond.(--deleted--) Rene Kanters Chemistry Department University of Richmond KANTERS@URVAX.URICH.EDU =============================================== Date: Tue, 03 Mar 92 22:51:24 EST From: Rami Osman Subject: Re: The future of ab initio Hi Jan, There are really two parts to the answer, but this is perhaps because of the ambiguous definition of ROUTINELY. If Routinely means just being able to run such a job and the results will arrive in a few days (or a few weeks?) it would be of limited use to me. I would be interested in calculating a good quality potential energy surface of a large molecule, say an isomerization of a tripep- tide, within a reasonable time limit for example a few hours. Such potential reactions, which is one of my interests. I guess at the end of the survey you WILL tell us where we can get such a COMPUTER. Regards, Rami Osman ============================================== Date: Tue, 3 Mar 92 23:17:52 -0500 From: fredvc@esvax.dnet.dupont.com Subject: RE: the future of ab initio (--deleted quotes of jkl@ccl.net and m10!frisch@uunet.UU.NET--) We have certainly come a long way from the time when calculation of the rotational barrier in ethane was worthy of publication as a JACS Communication. Dr. Frisch certainly provides a good benchmark for where we are. However, one would really like to complete such a calculation in 30 minutes or less!! Such a time scale, within a factor of 2-3, is what I believe to be the intended frame of reference for the question. FREDERIC A. VAN-CATLEDGE fredvc@esvax.dnet.dupont.com (--deleted--) ============================================== >From pvrs@organik.uni-erlangen.de Wed Mar 4 06:49:57 1992 From: Paul Schleyer Subject: Re: The future of ab initio Date: Wed, 4 Mar 92 12:43:58 MET (--deleted jkl@ccl.net quote--) Dear Dr. Labanowski, Such capability would open up a very large area of chemistry, particulalarly with regard to the combination of computations on middle large molecules with experiment. HF and MP2 levels are very good for structures and the computation of many properties (e.g., vibrational and nmr spectra) which would often be decisive in helping the experimentalist. This applies both to pure and more applied research areas. I do not think in terms of "commercial R & D applications" in my ivory tower. But do tell me when it will be possible to carry out such calculatins! What is underway? Sincerely, Paul Schleyer (--deleted--) ============================================= Date: 04 Mar 92 10:47:02 EDT From: Subject: Large scale computations E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 (1) 44 27 42 08 UDIM018 at FRORS31 Although Dr. Labanowski requested reponse his large scale computation question to be sent to his own address, Mike Frisch's comment on using G90 on this size permitted me to respond with a question. First, a lot of people will be doing large scale calculations of the 500 CGTO size in the future as well as presently, and routinely. We are working on zeolite substructures and reactions occurring on these models, and that gets big. Certain transition states are correlation sensitive and given the "ifyness" of using a model system our protocols for the present will not go beyond SCF DZP optimizations followed by a MP2 estimate. Currently distributed codes like Gaussian90 can handle this kind of calculation in direct. Note that it is not so much the single point calculation time which is en jeux but the geometry optimization times. Even for relatively small systems these can go on for days or weeks in work station environments. It would also be useful to have work station clusters capable of speeding up that operation. Now the question and remark. The supercomputer environment is one configuration but people are building up clusters of work stations. In some types of problems (molecular dynamics, quantum Monte Carlo) some people are running 20 or more RS/6000 on the same problem. Many labs or Universities have unused units in the night, weekend or vacation periods and those who have work to do groan when they see a machine inactive. Where are people going on this type of clustering with regard to "standard" quantum chemistry codes, especially in direct SCF or MP2? This is of current interest in France and plans are to go "cluster" for the next few years. Any information from the other side of the Atlantic would be appreciated. E. M. Evleth ================================ Date: Wed, 4 Mar 1992 05:55 CST From: Andy Holder Subject: A gadfly forever..... I haven't run this out yet, but I'm sure that AMPAC using the highly successful AM1 method could perform this calculation in a much shorter time than an ab initio calculation with reasonable results. I think the discussion should refocus on "What can be done now that couldn't be done before?" Semi- empirical methods can now do calculations on reasonably sized polymer chains or biomolecules efficiently. Oh, well. Andy Holder (--deleted--) =================================== From: Dale Moberg Message-Id: <9203041441.AA00301@axon.cis.ohio-state.edu> Subject: comp chem tutorials in Columbus? (--deleted--) A molecular biologist and myself have considerable interest in understanding comp chem potential for biopolymers, especially surface contour potential maps along stretches of DNA, RNA and polypeptides. (--deleted--) Dale Moberg ====================================== Date: Wed, 4 Mar 92 09:59:05 -0500 From: philk@hermann.polymer.uakron.edu (Phil Klunzinger) Subject: ab initio wish list I am currently using semi-empirical calculations for modulus and normal mode analysis on a series of polymers. I would like to replicate a few of these calculations using ab-initio calculations, if only 1) i knew more about them, 2) they were readily aviable, 3) i could do them so quickly my thesis would not be delayed (unless of course the data is so good they make my thesis). Philip E. Klunzinger (--deleted--) ===================================== Date: Wed, 04 Mar 92 17:24 FWT From: "Roland Wiest . . . 88-41-61-28" (Lab. Chimie Quantique, BP 296, F-67008 Strasbourg Cedex) Subject: Re: The future of ab initio Dear Jan, We CAN, already, ROUTINELY do calculations with 500 contracted GTO's Our ASTERIX set of programs (see: i) Ernenwein,R. et al, Comput. Phys. Comm. 58(1990)305 ; ii) Rohmer,M-M.et al, id,60(1990)127 ; iii) Wiest, R. et al, id, 62(1991)107 ) allows such a calculation like (V 10 O 28) anion with 1404 GTO's and 578 CGTO's. (see Rohmer et al, IJQC 40(1991)723 ) Other calculations, most of them in the organometallic chemistry area have been done or are in progress, in relation with problems encountered by chemists in either homogeneous catalysis or crystallography (electron deformation density or molecular electrostatic potential), photochemistry, PE spectroscopy, excited states, reactivity, etc, etc.. For more information, see recent papers in SCI or Chem Abs, under author names like Benard,M., Rohmer,M.M., Dedieu, A., Veillard, A., Daniel, C. etc. All this is more or less fondamental research, with helas, no direct interaction with R. & D. industrial departments. The real question, in vue of problems arising from experimental chemistry, is " How to do easily, and rapidly, calculations involving 1000 or 1500 or 2000 CGTO's, in order to give a realistic description in organometallic or other "big" systems like polypeptides, aminoacids etc." I hope this parcellar answer will help you to appreciate the magnitude of the problems treated Friendly Roland =========================================== Date: Wed, 4 Mar 1992 13:25:11 -0500 From: zheng@retina.chem.psu.EDU (Ya-Jun Zheng) To those who are interested in the performance of molecular mechanics on hydrogen bonding interactions. The following reference may be very interesting. J. Mol. Struct. 1992, 265, 179. For system like CH3COO-...3H2O, the molecular mechanics results can be 10-14 kcal/mol off the experimental value. Yajun Zheng ========================================== Date: 03/05/92 08:14:34 From: "Joe Golab" (--deleted--) If I could routinely perform calculations of the type you describe, I would want more immediately. (HAHA.) I am assuming that by routine, you mean that the hardware/software combination is efficient, which for me implies I will get the answer within 24 hours or less. Mainly, we would perform more realistic simulations of reaction dynamics. We would survey a potential energy surface to a higher degree of accuracy. We would use the method to automatically incorporate correlation in a search for transition states (and try to "firmly" answer whether this TS was unique). We would hope that thermochemical properties thus obtained would be better than now. We would probably also start to look@this new thing called "ab initio" molecular dynamics for polymeric species. We would also most probably become very interested in better metal surfaces, i.e. either "less effective" ECPs or larger metal clusters or larger adsorbed/absorbed species or all of the above or any combination. Obviously, Jan, these opinions are mine and in no way reflect research I am engaged in@Amoco Chemical Company, Amoco Corporation or any of its subsidiaries. Hope all is well. :Joe =============================== Date: Tue, 3 Mar 92 15:36:31 -0800 From: ross@zeno.mmwb.ucsf.EDU (Bill Ross) Subject: Re: The future of ab initio I would do more nucleic acids and ion-nucleic complexes for force field parameterization. Currently I'm doing optimizations & charge calculations on various base pairs. Bill Ross UC San Francisco ================================ Date: Tue, 3 Mar 92 19:45:00 EST From: chan@tristan.TN.CORNELL.EDU (Ernest Chan) Subject: future of ab inito calculation Although I have never done any ab initio calculations, I will love to use HF method to study more complicated chemical reactions. If your basis set is larger still, say 5000, quantum drug design seems like a nice and useful application. -Jack Chan ================================ Date: Tue, 3 Mar 1992 19:58 EST From: "To help us serve you better, please take a number..." Subject: the future of ab initio (--deleted--) (2) As to what would we do if we could routinely run very large ab initio jobs...we are a group who both consumes and develops ab initio code. We have a joint NIH grant with an organic chemist to study the structure and reactivity of taxol. We are restricted to non-QM methods for the most part and in practice are limited to semi-empircal methods even for crude models of the system. We'd be overjoyed (and back in our element) if we could do ab initio calculations on taxol. In general, we could have more involved interactions with our organic colleagues if we had access to ab initio code for very large systems. Sincerely, Michelle M. Francl Bryn Mawr College Internet: mfrancl@cc.brynmawr.edu ============================ Date: Tue, 3 Mar 92 16:54:32 -0800 From: mecolv@snll-arpagw.llnl.gov (colvin michael e) Subject: Large ab initio calculations. Jan, On a semi-routine basis I am running 500 basis function single point SCF and MP2 calculations (a 656 basis functions, 1968 primitives, no-sym direct SCF is currently queued up) as well as 250 basis function SCF optimizations and 120 basis function MP4 single points. I would certainly like to be able to run these on a truly routine basis, that is, on my workstation. I am involved in a number of projects working with medicinal chemists to help understand the biochemistry of pharmaceutical drugs. To the medicinal chemists any molecule with less than a hundred or so atoms is "small", so it's been a challenge to find systems small enough to fit on our Y-MP. Of course there are lots of other complications in modeling biochemical systems, such as aqueous solvation effects, which will make these systems even more computationally demanding. For example one project involves studying the anti-cancer drug cyclophosphamide and its active metabolites. Since these compounds contain several exotic moeties such as phosphorodiamides, semiempirical methods don't work all that well, so we're forced to use ab initio methods. So far this has involved trying to determine the aqueous-phase protonation state of the metabolites, looking at the reaction enthalpies of deactivating reactions and exploring plausible reaction pathways. What we'd really like to is get a handle on the DNA cross-linking which will require much larger calculations. We did a single point sto-3g SCF calculation on 6 base pairs of DNA involving 1473 basis functions, but we can only afford this sort of calculation once in a long while. To try to make such calculations more routine, we have been working for several years to create a parallelized SCF, SCF gradient, and MP2 package. We have a "production" version of the first two parts running on an NCUBE/2 and IPSC 860. The performance is pretty good, but the machines are sufficently cantancerous to make "routine" runs difficult. If you'd like more info on the big calculations just send me some mail at mecolv@sandia.llnl.gov. If you're intersted in more info on the parallel QC code send questions to Curt Janssen (cljanss@sandia.llnl.gov). --Mike Colvin Sandia National Laboratory Livermore, CA =========================================== Date: Wed, 4 Mar 92 09:40:36 EST From: states@ncbi.nlm.nih.GOV (David States) Subject: Re: A gadfly forever..... (How far can you push semi-empirical methods?) |> Andy Holder writes: (--deleted--) To me this is a real opportunity. Empirical energy simulations of biological macromolecules have improved incrementally over the past decade, but many significant terms in the potential energy function are ignored, particularly polarization effects (charge induced dipole terms, cooperativity in hydrogen bonding etc.). These terms are significant compared to kT. It does not make alot of sense to me to run longer and longer simulations when you know the underlying potential function is flawed. Semi-empirical methods offer a real hope of addressing some of these issues. So what are the largest peptide systems that have been evaluated with semi-empirical methods? Have any been done with Monte Carlo averaging over nuclear conformations? Has anyone been bold enough to attempt dynamical simulations based on semi-empirical PE functions and derivatives? David States National Center for Biotechnology Information / National Library of Medicine ======================================= Date: Wed, 4 Mar 92 08:35:06 PST From: case@scripps.EDU (David Case) Subject: Re: A gadfly forever..... (How far can you push semi-empirical methods?) David States wrote: (--deleted--) I too would enjoy hearing from people that know about this. When I wrote a review a few year ago [in "Conformational Analysis of Medium-Sized Heterocycles", edited by Richard Glass] semiempirical methods seemed to have very poor performance for non-bonded interactions and hydrogen bonds -- things that are crucial to most peptide and protein simulations. Errors in barriers to rotation about bonds, or in ring conformations (e.g. planar cylcopentane) were also common. But at that time, not much had been published with AM1, although that appeared to give improved results in these areas. Are semi-empirical methods now meeting Dave States' desires? David A. Case (--deleted--) ================================ Date: Wed, 4 Mar 92 08:35:38 PST From: d3f012@gator.pnl.GOV Subject: large scale semi-empirical calculations Andy Holder writes:(deleted) David States writes:(deleted) We routinely do INDO/s SCF/CI calculations on the chromophores of bacterial photosynthetic reaction centers that involve ~600+ atoms, 1500+ electrons, and a few thousand configurations (single-excited) in the CI. These calculations also have included portions of the surrounding protein. We have been doing Molecular Dynamics with forces from a semi-empirical Hartree Fock solution. Mark A. Thompson (deleted) d3f012@pnlg.pnl.gov ================================ Date: Fri, 06 Mar 92 08:36:37 +0900 From: kddlab!vega.rc.m-kasei.co.jp!mei@uunet.UU.NET (Murakami Akinori) Subject: Re: The future of ab initio Thanks to Gaussian inc. and IBM >> What would you do if you could ROUTINELY perform ab initio (--deleted--) >> HF/6-31G* on C30H62 with no symmetry (574 basis functions) takes well under (--deleted--) >> Michael Frisch We have following timing data of Gaussian90 on a IBM RS6000/550 which is little bit expensive. IBM official Mflops is 25. unit[minute] Molecule Basis SCF+grad C10H8S2 132 28 C14H12 150 29 C18H12S2 212 109 We are running 200 basis( 20~30 atom) calculation routinely. But we have to use about 300~500 basis on Metal complex calculation in our catalyst research. We want to optimize 500 basis molecule, it will take about 1000 hour on 25 Mflops WS. One month for one calculation is not possible in our research center. Akinori MURAKAMI Mitusbishi Kasei Corpration Yokohama, JAPAN ===================================== Date: Sun, 8 Mar 1992 23:13 EST From: "DOUGLAS A. SMITH" Subject: burning time on supercomputers In response to Jan Labanowski's question, we have one area which still seems to defy current resources, or at least pushes them to the extreme. We have been studying hydrogen bonding in a series of di- and triamides which involve from 8 to 20+ heavy atoms, using molecular mechanics to probe the potential energy surface (you guessed it- the multiple minimum problem). We are now at the stage of beginning to take our tens of minima for each compound, found using the AMBER force field in MacroModel, and submitting each for ab initio single point and geometry optimization. Hydrogen bonding requires massive basis sets for molecules of this size - a recent paper by Pople suggested that RHF/6-31+G** was a minimum requirement, although they did their optimizations at RHF/6-31G* single points at MP2/6-31+G**. We want to also do RPAC calculations of NMR spectra and chemical shift tensors, so the wavefunction must be a good one. These last few requirements are not trivial in and of themselves, but when coupled with 8-10 compounds with from 5-40 minima each, the need for resources just explodes. Regardless, we are trying. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email fax0236@uoft02.utoledo.edu From chemistry-request@ccl.net Fri Mar 13 22:01:38 1992 Date: Sat, 14 Mar 1992 03:11:50 +0100 From: Ole Swang Subject: coupled cluster methods question To: FAX0236@uoft02.utoledo.EDU Status: R "Best method for open-shell systems" .... This seems a rather vague concept to me. A lot of open-shell systems are very well described by RHF or UHF procedures. The CC method is an excellent method for describing dynamical correlation, whether the zeroth-order wavefunction is open- or closed-shell, but if low-lying excited states exist (like in a transition state) the only qualitatively correct description will be a multiconfigurational SCF (MCSCF) model - eventually refined by a multireference CI calculation (unfortunately, as far as I know nobody has implemented a general multireference coupled cluster algorithm as yet). Generally, a double-zeta valence plus polarization basis set (like, say 4-31g*) should be thought of as a minimal basis set for calculations involving correlation (something like STO-3g for Hartree-Fock). There is, of course, a practical limit for the size of the systems which can be studied using CC, or any other ab initio method. Where the limit goes is depedent of the available resources. You don't specify what kind of problems you want to look into, but in most cases a CC treatment is a factor 3 or 6 or something more expensive than a CI treatment. (there shouldn't be an exponential differennce betweeen the two).