From kb7@tower.york.ac.uk Fri Dec 10 07:54:34 1993 Received: from leeman.york.ac.uk for kb7@tower.york.ac.uk by www.ccl.net (8.6.4/930601.1506) id HAA03888; Fri, 10 Dec 1993 07:22:28 -0500 Received: from tower.york.ac.uk by leeman.york.ac.uk with SMTP (PP) id <13092-0@leeman.york.ac.uk>; Fri, 10 Dec 1993 12:08:37 +0000 Received: by tower.york.ac.uk (920330.SGI/920502.SGI) for @leeman.york.ac.uk:CHEMISTRY@ccl.net id AA16548; Fri, 10 Dec 93 12:21:30 GMT Date: Fri, 10 Dec 1993 12:01:05 +0000 (GMT) From: K Bryson Subject: Summary on DNA structure analysis software. To: CHEMISTRY@ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, this is a summary of my findings on Nucleic Acid structure analysis software ... Original Posting ---------------- > Hi, > A previous message on a database for Nucleic Acid > X-ray structures has got me wondering about how much software > is out there to analyse nucleic acid structures. > I know of R.E. Dickerson's Newhelix93 program for static > structure analysis but do not know any other programs for the > analysis of features not provided by this program such as > Shear and Opening Parameters between base-pairs. > For trajectory analysis I know G. Ravishanker has a > program called 'Curves, Dials and Windows' and R. Lavery has > a program called CURVES 3.0 ( not sure if it's the same program ), > but I do not have sources or know the availability of these. > > I would be grateful to receive information on these types > of packages, personal feelings about their use, and sources to > obtain them. > If the response is fruitful then I will form a summary of > programs, their features and ftp sites. > > Thanks, > Kevin. From nauss@ucmodl.che.uc.EDU ---------------------------- For my dissertation work, I analyzed DNA structure in terms of individual base pairs. To describe the orientation of any two bases (base paired or not) I used three translations and three rotations from a transformation matrix. Furthermore, my algorithm was reversable to allow building of DNA polymers (and RNA for that matter) from the translation and rotation parameters. The publication of the paper has been delayed for numerous reasons ...... You could also look up my dissertation entitled "Conformational Analysis of Polynucleotides at the Base-Base Level". This work was done under the supervision of Prof. Wilma K. Olson at Rutgers University. I believe since then another of her students has advanced the algorithm but I do not believe she is giving the program out yet. From nauss@ucmodl.che.uc.EDU ---------------------------- One other thing, I believe the trajectory analysis by G. Ravishanker is an adaptation of Lavery's curves. You could, in theory, adopt any analysis program to analyze a trajectory by simply reading each frame and compiling the results. From reinert@VAX.mpiz-koeln.mpg.d400.de --------------------------------------- Write to: Richard Lavery Laboratoire de Biochimie Theorique URA 77 CNRS Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie Paris 75005 France Tel: 33 1 43 25 26 09 Fax: 33 1 43 29 56 45 to obtain CURVES and JUMNA From ravishan@swan.wcc.wesleyan.edu ----------------------------------- We have a general MD analysis package, with a total of 30 to 40 tools to extract various properties of the system - solute properties, solvent analysis, DNA specific, protein specific and protein-DNA complex specific tools. One component of this is called the dials and windows. We have modules to perform persistence analysis for bending analysis of DNA, other forms of this called the bending dials, new ways of measuring the groovewidths, extracting the "spine of hydration" in the grooves and doing statistical analysis on them amongst other things. We have several other utility modules (over 20) that perform very GROMOS specific tasks, such as coordinate coversions. We are adding a new set of tools to do NMR property calculations, such as the nOe buildup curves, T1, T2, order parameters, and coupling constants using generalized Karplus equation. We have also beefed up the graphics considerably so the current version produces graphics through our general-purpose scientific graphing facility called DEVINE Graph. The next distribution will include MD Toolchest and DEVINE Graph (currently supports X11 OSF/Motif and Postscript) and we are planning to get it out by Feb 1994. We had plans to get it out in Nov. but we are behind. If you need more info, please let me know. Thanks. From ravishan@swan.wcc.wesleyan.edu ----------------------------------- I also wish to mention that our program set can be used to analyse static structures, either one by one or in a compare mode and we have applied our DNA tools to analyse all the decamers and dodecamers in the NDB maintained by Helen Berman. From ravishan@swan.wcc.wesleyan.edu ----------------------------------- ............... The code currently runs on SGI, IBM RS6000 and CRAY Y/MP. With minor modifications, one should be able to port to other machines. We will soon port it to run on a PC running NeXTStep. It is written in Fortran 77 and C. The underlying program that produces the variables for dials and windows is Lavery's CURVES. The graphics is done by dials and windows. However, one can interface it to any program, say newhelix with some effort. I am trying to contact Dickerson to get the current NEWHELIX, so that we can put in the necessary modules (but require users to get NEWHELIX from Dickerson). The MD Toolchest library is so organized and a template fortran program is given in the distribution that tells you how you can write your own application easily, by letting the MDTC library do all the work of processing the coordinates etc. From Patrick.Bultinck@rug.ac.be Fri Dec 10 10:54:36 1993 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id KAA05104; Fri, 10 Dec 1993 10:25:48 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA06636 (5.65c/IDA-1.4.4 for ); Fri, 10 Dec 1993 16:25:23 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA20773; Fri, 10 Dec 93 16:23:03 +0100 Date: Fri, 10 Dec 1993 16:22:45 +0100 (MET) From: Patrick Bultinck Sender: Patrick Bultinck Reply-To: Patrick Bultinck Subject: summary on population analysis To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 18160 On Fri, 3 Dec 1993, I, Patrick Bultinck, wrote: > > I have performed some population analysis calculations on covalent > molecules using ab initio Hartree-Fock. I performed MPA and LPA (mulliken > and lowdin). The results were often miles apart. The reason, I think, is > the fact that every value for n in S^nPS^(1-n) will do for defining a > population analysis formula. > I do no longer believe very much in the use of population analysis for > determining atomic charges for atoms in a certain molecule. This > disbelieve became bigger when last year, during my graduation thesis, I > studied calculations of dipole moments. Indeed I remembered the formula > DIP. MOM.=sum(atomic charge*R), sum over all atoms. I thought I could see how > good PA was by using the PA results to determine the dipole moment (apart > from the one calculated with the wavefunction). I calculated the different > cartesian components of the DM, since PA gave me the charges and I knew > from my input what the cart. coordinates of the atoms were. By putting > together the cart. comp. of the DM I got to a value of the total dipole > moment. Needless to say that the value was sometimes miles apart from > experiment and from the wave-function derived dipole moment...(using RHF > and RHF defined PA formulas) > > My question is : > What is the use of the S^nPS^(1-n) derived population > analysis ? > Is there something crazy about my argumentation to say that PA is not to > be trusted very much ? (esp. where I used the formula for the DM using the > PA results...) > > Thanks for replies.... > > Patrick Bultinck > University of Ghent > E-Mail : Patrick.Bultinck@rug.ac.be > > > Thanks everybody who helped me out, or more exactly convinced me of the fact that PA is a strange thing. Indeed some people were right to state that looking at atoms in a molecule as spheres is dangerous, but I thought about that very fact when I was making my thesis and suspected that even that approx. could not be guilty of the (very) big deviations. IMPORTANT : there was a mistake in Mr. Stones reference, the correction can be found below Patrick Bultinck University of Ghent E-Mail ---> Patrick.Bultinck@rug.ac.be From: carlos@extreme.bio.cornell.edu (Carlos Faerman) To: Patrick.Bultinck@rug.ac.be Subject: charges, dipoles,... Patrick I recommend that you read Anthony Stone's papers on this very subject. He is the expert in this field since he proposed a better way to partition the electron density among atoms and therefore provide a better set of partial charges. He is certainly not alone in this club of disbelievers of Mulliken analysis. Richard Bader has also advocated a very fancy partition scheme to get decent charges. Richard Bader is at McMaster Univ. , Hamilton , Canada while Anthony Stone works in Cambridge , UK Perhaps reading their numerous papers might clarify/answer your ideas/questions Regards Carlos From: smb@smb.chem.niu.edu (Steven Bachrach) To: Patrick.Bultinck@rug.ac.be Subject: Re: POPULATION ANALYSIS Your results are exactly as expected - population analysis defined in terms of orbital populations is garbage. I have recently ritten a review of population analysis in Reviewss of Computational Chemistry, volume 5 which was just published. This review goes into some detail on the failings of traditional populations methods. Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 smb@smb.chem.niu.edu From: Lipkowitz Subject: RE: POPULATION ANALYSIS To: Patrick Bultinck For your information, there is a good review, albeit low level, of population analyses in Reviews of Computational Chemistry, Volume 5, chapter 3 by S. Bachrach. The book is published by VCH Inc., 1994....ie, it will be out on the market soon. Kenny Lipkowitz. _______________________________________________________________________________ From: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU Subject: To: Patrick.Bultinck@rug.ac.be Dear Patrick: Reliable net atomic charges can be found by fitting the molecular electric potential obtained by ab initio quantum mechanical methods. The idea is to find the best atomic charges which will reproduce the potential. Program PDM93 also allows atomic dipoles/quadrupoles, bond dipoles, and addition of lone pair electron sites if necessary in order to fit the electric potential. A particularly useful feature of the program is the transparent way in which dependency conditions are specified. I append information about this program. -Don Williams Program PDM93, Potential Derived Multipoles The following is a brief description of this program. Molecules interact with each other via their electric potential. PDM93 finds optimized net atomic charges and other site multipole representations of the molecular electric potential based on a variety of models. The program is easy to use, flexible and powerful. Results are obtained in a single iteration and a complete error treatment is made which includes estimated standard deviation and correlation of variables. The program is written in Fortran 77 and runs on Unix, Vax, and other computers with F77 capability. Program PDM93 has a unique combination of features: o general sites, not necessarily at atomic locations o each site may have any combination of monopole, dipole, or quadrupole o bond dipole model is supported o restricted (along the bond direction) bond dipole model is supported o provision for site dipole vectors in sp2 or sp3 directions o selected fixed atomic charges o selected groups of atoms with fixed charge o atomic charge equalities or symmetry relations o rotational invariance of site charges o provision for optional foreshortening of X-H bonds o comparison with Mulliken charges and Mulliken electric potential o direct input from Gaussian-92 o generalized input from other quantum mechanics programs o automatic generation of electric potential grid points o provision for custom generation of grid points o on-line program manual o comprehensive examples are provided A review of potential-derived charges may be found in Reviews of Computational Chemistry, Vol. II, pp. 219-271 (1991). For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. Tel:(502)588-5975 Fax:(502)588-8149 E-mail:dewill01@ulkyvx.louisville.edu ----------------------------------------------------------------------- Ordering information Program package consisting of manuals, Fortran-77 source files, and demonstration example files....................................$2,000 Special discount price is available to academic institutions ........$495 Choose the preferred method of shipment: Via ftp, purchaser furnishes valid ftp address................n/c Via magnetic media, specify type..............................$20 DC6150 tape cartridge, unix tar format or MP120 tape cartridge (8mm), Vax backup format or 9-track 1600 bpi ascii tape or 9-track 6250 bpi ascii tape Make check payable to the University of Louisville. ------------------------------------------------------------------------- From: gg502@fermi.pnl.gov Subject: Re: POPULATION ANALYSIS To: Patrick.Bultinck@rug.ac.be Mulliken himself said "Population analyses must be used with appropriate caution... even though the method is faulty, it has the insidious appeal of always giving definite numbers." Mulliken and Lowdin analyses are based on completely arbitrary partitioning of what space belongs to which atoms, and are strongly dependent on the basis set itself as well. It is even possible for Mulliken population to be negative, which is pretty nonphysical. These problems have long been known, but many many people still take them as gospel. They certainly can be meaningful indicators in selected cases, which must be thoughtfully analyzed, but the usual blind trust is entirely inappropriate. Bader and others have developed population analyses schemes that try to eliminate some of the problems with the traditional S^n P S^(1-n) methods. Bader's method uses numerical integration to locate zero flux surfaces in the density which are the basis for defining "atoms" in his scheme. This is _much_ more expensive than a couple of matrix multiplications, and people have observed cases where some atoms don't have "atomic basins" (the region enclosed by a zero flux sheet). So population analysis in general is a tough problem and the methods like Mulliken and Lowdin are about the simplest possible (and therefore most troublesome) approach. -- David E. Bernholdt | Email: de_bernholdt@fermi.pnl.gov Molecular Science Research Center | Phone: 509 375 4387 Pacific Northwest Laboratory, P.O.B. 999 | Fax: 509 375 6631 Richland, WA 99352-0999 | From: ole.swang@kjemi.uio.no To: Patrick.Bultinck@rug.ac.be In-Reply-To: Patrick Bultinck's message of Fri, 3 Dec 1993 16:14:35 +0100 (MET) Subject: POPULATION ANALYSIS >Is there something crazy about my argumentation to say that PA is not to >be trusted very much ? Certainly not, in my view. Many chemists have an urge to assign charges to atoms within a molecule. However, such charges do not exist as observable quantities (eigenvalues of the wavefunction, quantum mechanically speaking), so anyone insisting on having them will have to rely on one arbitrary scheme or another..... Richard Bader (Hamilton, Canada) has suggested a scheme based on topological analysis of the electron density. Space is divided into parts "belonging to" different atoms or fragments in a molecule. The results look sounder than Mulliken ones. Still, some peculiar results come out from time to time, especially when partitioning space between atoms that differ greatly in electro- negativity. Also, this approach rely on a good electron density to start with. Population analysis is a controversial and interesting topic, but still most people (including me) use Mulliken because it's there in the software, it is much better than nothing, and perhaps more important, it is well tested: Even if it is far from ideal, it's area of validity is more or less known. Just some thoughts, Ole Swang. From: EDGECOMK@QUCDN.QueensU.CA To: chemistry@ccl.net Subject: popln. analysis and dipoles Patrick B.'s comments on population analysis and dipole moments strike a cord. I have heard these complaints(and made some myself) for a number of years. 1) the choice of divison of the overlap population is arbitrary... various lines of thought have gone into the derivation of literally hundreds of methods of doing this but the bottem line is that you do not have a quantum mechanical operator for the population in an 'orbital' on a particular atom that 'belongs' to that atom. Perhaps the most attractive methods are those that arise through the use of quantum mechanics, do not use arbitrary boundaries and as well apply to the total density. (eg. Richard Bader et al's theory of mol. structure) 2) the 'charge' on an atom is not a point charge, this is a gross assumption that in itself can lead to large errors. It appears to arise from the conceptually appealing picture of nice spherical atoms in molecules. The density is, however, not spherical around each atom in a molecule. Thus, using a point charge model with populations calculated through arbitrary division of the overlap populations has a good chance of giving poor results. The above being said, these different methods of treating the problem of population analysis has led to a lot of chemical insight for various problems. You must keep the weaknesses in mind when choosing an approach. Any other thoughts on this? Ken Edgecombe ----- End of the message ----- From: ryan@phmms0.mms.smithkline.com (Dominic Ryan) To: chemistry@ccl.net Subject: Population analysis As was pointed out, population analysis is not unique. There are a host of methods available for partitioning density between sites. One must ask what the charges will be used for. In a force field context an atomic charge is simply one more fudge factor available in the system for tuning to get the 'right' answer. Early days of force field development concentrated on intramolecular energies, in vacuo at that. After you make pretty good guesses at bond stretching and angle bending components (and cross terms when part of your flavor of force field) you are left with torsion terms, VDW terms and charges. Early work derived VDW terms from rare gas data in part and from crystal packing (making allowances for the differences one sees there in x-ray, electron and neutron diffraction). One is generally left then with torsions and charges (VDW terms are also modified and combining rules are modified in Tom Halgren's work). You try to assign chemically sensible charges and tweak the torsion terms until conformational energies reproduce your reference states (quantum mechanical, and experimental). More recently there has been greater emphasis on intermolecular energies (lets ignore solvation for now). These are dominated by electrostatic forces. Now one needs to worry more about getting both chemically sensible charges and charges that will give the 'correct' interaction energy which must be taken from high level QM where one needs to worry about basis set effects etc. A relatively recent method of defining atomic charges calculates the molecular electrostatic potential around a molecule and constrains the charges to reproduce this distribution as much as possible. This has the advantage of in principle reproducing the bulk of the interaction energy between two molecules, including the anisotropy. In practice there are limitations here as well, and in small molecules particularly (H2O) a set of atom-centered charges in not sufficient to adequately describe the potential. One advantage of using 'fitted' charges is that the dipole (and higher order molecular multipoles) are well reproduced. There is a *lot* of literature on this approch now. Check out Reviews in Computational Chemistry, vol. 2 for a recent review. Bader's method of partitioning charge is consistent but leads to a different picture of atomic charge from the fitted methods. Neither one is *wrong* but they look at different things. ___________________________________________________________________________ M. Dominic Ryan (215)-270-6529 SmithKline Beecham Pharmaceuticals Headers may be WRONG, do NOT use reply, use: ryan%phmms0.mms@sb.com From: Lipkowitz Subject: Population Analysis To: Comp Chem List Netters: There has been, and remains, controversy about how to partition electrons on atoms for population analysis. To help me understand what's going on, Don Boyd and I asked Steve Bachrach to write a book chapter on that topic. See Reviews in Computational Chemistry, Volume 5, eds. K. Lipkowitz and D.Boyd, VCH Publishers Inc., New York, 1994 ( available in January). Kenny From: Gustavo Mercier Subject: Re: POPULATION ANALYSIS To: Patrick Bultinck Hi! To add to the discussion... In the 70's when the electrostatic potential became popular to explain molecular reactivity, it was very common to use MK derived charges to compute the potential from "large" molecules. It was very clear then that in many cases the dipole computed from the charges was poor. Nevertheless, the concept was useful, and in spite of poor dipole moments the TOTAL energy computed with the charges for a CONGENERIC family of molecules could be used to reproduce trends in chemical reactivity. In these cases systematic errors probably were controlled by only comparing SIMILAR molecules. But when is similar "dissimilar"? mercier mercie@cumc.cornell.edu From: Anthony Stone Subject: Population analysis and dipoles To: chemistry@ccl.net Population analysis and dipole moments The dipole moment of a molecule can be expressed in terms of atomic moments as sum (atom charge)*(position) + sum (atomic dipoles). This is exact if you define things correctly, but the atomic dipole values will depend on your choice of definition for the atomic charges. The atomic dipoles are usually significant, whatever definition you use for the atom charges, so if you leave them out you will get rotten molecular dipole moments. An exception to this is potential-fitted point charges, which give quite good values for the molecular dipole, but they achieve this by representing atomic dipoles by charges on nearby atoms, so the potential isn't very good in the neighbourhood of a dipolar atom. The Distributed Multipole Analysis procedure, described by Stone & Alderton in Mol. Phys. 110, 123 (1984), generates charges, dipoles, etc. from a wavefunction in a consistent manner (i.e. so that the overall molecular moments are correct for the wavefunction), and in such a way that the higher atomic moments are as small as possible. It is included in the Cadpac program. Bader's partitioning, mentioned by Ken Edgecombe, is much more elegant but it leads to much larger high-rank moments, which is an inconvenience for most applications. For a more general discussion see Stone & Price, J. Phys. Chem. 92, 3325 (1988). Anthony Stone University Chemical Laboratory, Internet: ajs1@phx.cam.ac.uk Lensfield Road, Phone: +44 223 336375 Cambridge CB2 1EW, U.K. Fax: +44 223 336362 Thanks to those who have pointed out that I gave the wrong reference in my recent posting about population analysis and dipole moments. It should have been Stone & Alderton, Mol. Phys. 56 (1985) 1047. Anthony Stone University Chemical Laboratory, Internet: ajs1@phx.cam.ac.uk Lensfield Road, Phone: +44 223 336375 Cambridge CB2 1EW Fax: +44 223 336362 From uviqplco@cesga.es Fri Dec 10 11:54:37 1993 Received: from cesga.es for uviqplco@cesga.es by www.ccl.net (8.6.4/930601.1506) id LAA05723; Fri, 10 Dec 1993 11:13:32 -0500 From: Message-Id: <199312101613.LAA05723@www.ccl.net> Date: Fri, 10 Dec 93 17:11 MET To: CHEMISTRY@ccl.net Subject: Porting HONDO 8.x to vectorized FUJITSU VP Content-Type: text Content-Length: 256 Hello, We are looking for a vectorized version of HONDO8.x running on FUJITSU VP ( 2400 or similar ). Please, send us any contact address. Thank you. Dr. Luis Carballeira Physical Chemistry Lab. University of Vigo Spain e-mail: uviqplco@ds.cesga.es From szilagyi@miat0.vein.hu Fri Dec 10 12:08:17 1993 Received: from sztaki.hu for szilagyi@miat0.vein.hu by www.ccl.net (8.6.4/930601.1506) id LAA05825; Fri, 10 Dec 1993 11:26:44 -0500 Received: by sztaki.hu with SMTP (5.67a8/SZTAKI-3.13) id hG10387; Fri, 10 Dec 1993 17:25:17 +0100 Received: by miat0.vein.hu (5.61++/Vein-1.0) id AA25499; Fri, 10 Dec 93 17:26:44 +0100 Date: Fri, 10 Dec 93 17:26:44 +0100 From: Szilagyi Robert Message-Id: <9312101626.AA25499@miat0.vein.hu> To: chemistry@ccl.net Subject: Theoretical chemistry laboratory Cc: h8588szi@ella.hu X-Charset: US X-Char-Esc: 0 Dear Netters, we would like to install a theoretical chemistry lab here at University of Veszprem, Department of Organic Chemistry. This lab will be used by mostly undergraduate students and research fellows. Our plan is a X-window based network containing: SGI Indigo R3000 SGI IndyPC IBM PC's (about 10) with SVGA graphics. The other side of the coin is the softwares. We bought the following programmes: Gaussian 92 PCMODEL V4.0 GAMESS We think about the Spartan, but we have problems with the parametrisation (atom types definitions). We experienced, the upgrading of SGI workstations is much expensive, than buy a new one. Is somewhere such kind of installed laboratory ? Any advice greatly apprecipiated. Cheers Robert (Rob) From markz@chem.duke.edu Fri Dec 10 12:11:46 1993 Received: from duke.cs.duke.edu for markz@chem.duke.edu by www.ccl.net (8.6.4/930601.1506) id LAA05728; Fri, 10 Dec 1993 11:14:28 -0500 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.7G/4.1.3) id AA15298; Fri, 10 Dec 93 11:14:28 -0500 Received: from dna.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA17087; Fri, 10 Dec 93 11:14:26 -0500 Received: by dna.chem.duke.edu (5.64/2.12L/4.1) id AA00425; Fri, 10 Dec 93 11:14:21 -0500 Date: Fri, 10 Dec 93 11:14:21 -0500 From: markz@chem.duke.edu (Mark A. Zottola) Message-Id: <9312101614.AA00425@dna.chem.duke.edu> To: CHEMISTRY@ccl.net Subject: Fuzzy Clustering Hi! Can anyone out there direct me to any public-domain software for doing fuzzy cluster analysis? I am trying to analyze a set of DNA structures. Thanks! -mark ********************************************** * * * Mark A. Zottola * * markz@chem.duke.edu * * Department of Chemistry * * Duke University * * * * 'The fault, dear Brutus, lies not with * * ourselves, rather within our CPU's...' * * (with due apologies to W.S.) * * * ********************************************** From simkin@chemres.tn.cornell.edu Fri Dec 10 14:54:39 1993 Received: from chemres.tn.cornell.edu for simkin@chemres.tn.cornell.edu by www.ccl.net (8.6.4/930601.1506) id OAA07546; Fri, 10 Dec 1993 14:50:13 -0500 Message-Id: <199312101950.OAA07546@www.ccl.net> Received: by chemres.tn.cornell.edu (16.6/15.6) id AA28377; Fri, 10 Dec 93 14:48:58 -0500 From: boris simkin Subject: MC simulating To: CHEMISTRY@ccl.net (chemistrylist) Date: Fri, 10 Dec 93 14:48:57 EST Mailer: Elm [revision: 66.25] To whom who are interested in Monte Carlo simulation of solutions! Let me turn your attention to our review I. I. Sheykhet and B. Ya. Simkin "Monte Carlo Method in the Theory of Solutions" Computer Physics Reports, 12 (3) 67-133 (1990). I believe it is a good addition to the book of Allen and Tildsley. Below is the content for your convenience: 1. Introduction 2. The Monte Carlo method 3. The problem of ergodicity in the Monte Carlo method 4. Convergence of results 4.1. Criteria for achievment of convergence 4.2. Schemes for speeding up convergence 5. Boundary models, their distinguishing features and effects 5.1. Periodic boundary conditions. Cutting off the intermolecular interaction potentials 5.2. The shortcomings of the periodic boundary conditions 5.3. Free boundary conditions - the cluster approach 5.4. A boundary model in the form of a pure solvent 6. Calculation of the free energy 6.1. The perturbation method 6.2. Thermodynamic integration method 6.3. Umbrella sampling 6.4. Test particle method 7. Methods for approximating intermolecular interaction energies by analytical functions 7.1. The main techniques of approximating intermolecular interactions 7.2. Empirical methods for constructing the potentials 7.3. Non-empirical (ab-initio) methods for constructing the potentials 7.4. Semi-empirical methods for constructing the potentials 7.5. Inclusion of many-body contributions 8. Conclusion References Incidentally, our with Dr. I. Sheykhet book "Quantum Chemical and Statistical Theory of Solutions. A Computaional Approach" will be published in the beginning of the next year by Ellis-Horwood Publishing House, England. Later I will send the content of the book. Best regards Professor Boris Simkin, Department of Chemistry, Cornell University From BOYD_DONALD_B@Lilly.com Fri Dec 10 16:54:40 1993 Received: from Lilly.com for BOYD_DONALD_B@Lilly.com by www.ccl.net (8.6.4/930601.1506) id QAA08509; Fri, 10 Dec 1993 16:31:31 -0500 From: Received: from DECNET-MAIL (QSAR@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.2-13 #2311) id <01H6BK4ILMWG0000J7@INET.D48.LILLY.COM>; Fri, 10 Dec 1993 16:30:55 EST Date: Fri, 10 Dec 1993 16:30:54 -0500 (EST) Subject: Re: population analysis summary To: chemistry@ccl.net Message-id: <01H6BK4IN8S20000J7@INET.D48.LILLY.COM> X-VMS-To: INT::"chemistry@ccl.net" X-VMS-Cc: ME MIME-version: 1.0 Content-transfer-encoding: 7BIT Patrick Bultinck's recently posted summary mentions REVIEWS IN COMPUTATIONAL CHEMISTRY, Vol. V, which is available this month. Professor Steven Bachrach (Northern Illinois University) has an excellent chapter in it discussing many of the problems encountered when trying to interpret the meaning of data from the various traditional methods of population analysis. As Kenny Lipkowitz, co-editor of REVIEWS IN COMPUTATIONAL CHEMISTRY, pointed out, the chapter starts at an introductory level and then carefully examines each of the methods. The chapter is very high level in quality, content, and writing. D.B. Boyd From: BOYD DONALD B (MCVAX0::QSAR) To: VMS MAIL ADDRESSEE (INT::"chemistry@ccl.net") cc: BOYD DONALD B (MCVAX0::QSAR)