From d3f012@gator.pnl.gov Mon Oct 12 15:13:43 1992 Date: Mon, 12 Oct 92 22:13:43 PDT From: d3f012@gator.pnl.gov Subject: Argus User Manual is fixed To: chemistry@ccl.net Argus users: I finally have a postscript version of the User Manual that is small enough to be printed. The new file UserMan.ps is ~300K (previous file was ~2.5Meg), and is available via anonymous ftp from pnlg.pnl.gov (in the Argus directory). You can download just the file UserMan.ps if you already have the program. I have also included the new postscript file in argus.tar.Z One note on compressed files stored on VAX/VMS: The unix file argus.tar.Z loses the .Z suffix when I move it to the VAX. Hence, you must first rename the file argus.tar -> argus.tar.Z when you download it. Then, uncompress it, then, untar it. Sorry about the inconvenience. Mark ************************************************************************** Mark A. Thompson email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From grubi@nirvana.t30.physik.tu-muenchen.de Tue Oct 13 05:08:54 1992 From: Helmut Grubmueller Subject: On the use of Cut-off Schemes in MD To: CHEMISTRY@ccl.net Date: Tue, 13 Oct 92 9:47:05 MET Dear Netters, Arne Elofsson writes: > Let's assume that there is something really strange about > these simulations. What can we then do about it ? I have > a suggestion that involves a collaboration all over the world. > If every one spend some computing time on the same system, > i.e. the same peptide but different forcefileds, box sizes .. > Would we not be able to together solve this problem that is > important to all of ous. For practical reasons maybe it is > easier to limitate this kind of study to a few labs (five to ten). > If there is an interest in this kind of study I would > consider spending some time organize contacts. I think this > list is the best forum to discuss what should be studied and how. I strongly support the idea of a large-scale empirical check of the effects of the cut-off method. One has to careful, however, not to mix up physics/chemistry and numerics: It is one problem to find a *physical model* of a molecular system that approximates reality. It is another problem to find *numerical* algorithms/approximations to speed up simulations employing that model. Both problems are nearly independent and should therefore be discussed independently. The cut-off method was introduced to save computer time, and should therefore be regarded as an approach to the second, *numerical* problem. Note that this does not mean, that a cut-off-simulation is generally less accurate (as compared to reality) than one involving all Coulomb pair interactions. In many situations the opposite is actually the case (this is considered to be due to an imitation of shielding effects by the cut-off method). Consequently, the following remarks are meant to clarify the *numerical* aspects arising from the long-range character of the Coulomb interaction. 1) Many people working in this field seem to think that the only way to save computer time in doing MD-simulations in volvong long-range interactions is to employ one of the well known cut-off schemes available in most MD-packages. This is, however, not the state of the art. In recent years, a whole bunch of methods have been developed to speed up the simulations of multi-body systems considerably *without* any significant loss (i.e. significant in the course of MD-simulations) of accuracy. Generally speaking, these methods replace the tradeoff between efficiency and accuracy by a tradeoff between *memory requirement* and accuracy, which turned out to be a serious obstacle in former times. With the availability of very cheap memory chips, however, this limitation is vanishing. Two methods may suffice to exemplify this statement: a) The fast multipole method (FMM) by L. Greengard and V. Rokhlin is based on a sophisticated multipole expansion of the Coulomb potential. In contrast to the conventional method of summing up all pair interactions within the molecule, which requires of the order of (N^2)/2 operations (N being the number of charged atoms within the molecular system to be simulated), while the FMM is of order N. The constant of proportionality depends on the desired accuracy, which can be preselected. The FMM has already successfully been employed for MD-simulations. As could be expected from this scaling behaviour, the FMM turns out to be most efficient for systems with large numbers of atoms, whereas it is comparably slow for small molecules. If I remember correctly, the break-even lies in the range of 1000...2000 atoms. To my very best knowledge, the FMM can only be applied for Coulomb-like potentials (i.e. 1/r). This may turn out to be a disadvantage, if one tries to include shielding effects caused by atomic polarizabilities. References hereto: L. Greengard and V. Rohklin: "A Fast Algorithm for Particle Simulations", J. Comp. Phys., pp.325-348, vol.73, 1987 L. Greengard and V. Rokhlin: "On the Efficient Implementation of the Fast Multipole Algorithm", Research Report of the Yale University, Department of Computer Science, vol. RR-602, Feb., 1988 L. Greengard and V. Rokhlin: "On the Evaluation of Electrostatic Interactions in Molecular Modeling", Chemica Scripta, 29A, pp. 139-144, 1989 K. E. Schmidt and Michael A. Lee: "Implementing the Fast Multipole Method in Three Dimensions", J. Stat. Phys., submitted Edmund Bertschinger and James M. Gelb: "Cosmological N-Body Simulations", Computers in Physics, pp. 164-179, Mar./Apr., 1991 b) Multiple time step (MTS) methods employing distance classes: This method, (which is not to be confused with *variable* time step methods), has also been successfully employed for MD-simulations (see refs below) and turns out to yield speed ups comparable to the FMM. The MTS method can be regarded as a generalization of the cut-off method in that intaractions of atom pairs separated by a large distance are not completely neglected (as it is the case for the cut-off method); instead, these interactions (forces) are computed less frequently and are approximated by extrapolation. Since, in contrast to the FMM, a rigorous error-analysis of the MTS seems to be impossible, I carried out large-scale test simulations on a model-protein. The results show, that the method achieves a considerably higher accuracy (as compared to simulations of the same protein employing a cut-off of 10 A), while beeing even more efficient. In addition, the method can be flexibly adjusted to specific molecular systems to allow an individual tuning of the tradeoff between efficiency, accuracy, and memory requirements. References hereto: S. J. Aarseth: "Direct Methods for N-Body Simulations" (chap.12), in "Multiple Time Scales", Academic Press, 1985, 1st edition. Helmut Grubmueller, Helmut Heller, Andreas Windemuth, and Klaus Schulten: "Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-Range Interactions", Molecular Simulation, Vol. 6, pp. 121-142, 1991 Mark E. Tuckerman and Glenn J. Martyna and Bruce J. Berne: "Molecular dynamics algorithm for condensed systems with multiple time scales", J. Chem. Physics, vol. 93, #2, pp. 1287-1291, 1990 It is worth noting that both methods described above have also been successfully implemented on parallel computers (MIMD) and a speed up increasing nearly linearly with the number of processors was achieved. Furthermore, it seems to be possible to combine both methods in order to achieve even higher efficiencies. 2) The second point I want to make concerns the empirical comparison of different cut-off schemes by means of simulations carried out on identical molecular systems, as proposed by Arne Elofsson. As it turns out to be not at all a trivial matter, what quantities derived from the test-simulations should be compared in order to measure the numerical accuracy of the respective methods, I would like to make a few comments here: From a practical point of view, the results of an empirical test of the accuracy of different cut-off schemes should allow the estimation of the error of *relevant* physical quantities, that has to be expected when employing a particular scheme. Here, by *relevant* quantities, we mean observables, which are of central interest to the researcher carrying out a particular simulation. Since these depend entirely on the molecular system (model) under consideration, as well as on the questions the researcher wants to get answered, it is not possible to simply give a complete list of relevant quantities. It is, however, quite easy to give examples of quantities, which will most likely be *never* relevant in any MD-simulation, and which, given the quite obvious initial statement, should *not* be used to compare different cut-off schemes. One finds, however, that quite often just these irrelevant quantities are used as a criterion for the accuracy of some MD-algorithm under consideration. To be more specific, the test-quantities mostly encountered are atomic trajectories and conservation of total energy in a microcanonic simulation. Please note that I do *not* state that these quantities are not important. All I say is that these are not the quantities a biochemist is primarly interested in when performing MD-simulations. The problem that has to be solved is, therefore, to find a (possibly large) set of relevant quantities, which, in a sense, resemble typical situations encountered in the application of MD-simulations. Examples for quantities, that may be considered to belong to this set, and can thus be named 'relevant', are: * vibrational spectra * mean atomic positions and rms-fluctuations thereof * time autocorrelation functions of atomic positions/velocities * average values of different energy contributions (bond, Coulomb, etc.) * average values of radii of gyration * cross correlations of atomic motions * results of free energy computations * rates of conformational substate changes * configuration space densities (or densities in subspaces) (e.g. a histogram of the distance distribution between two atoms within the molecule) In my opinion, it could be useful for the project proposed by Arne, if one knew about what other quantities are considered relevant within the scientific community. I therefore ask you to help me to complete the above list by emailing me your suggestions (grubi@nirvana.t30.physik.tu-muenchen.de); I will post a summary. Please do not flood the mailing list with your suggestions. Helmut ============================================================================== Helmut Grubmueller Technische Universitaet Muenchen Theoretische Biophysik, Abt. T35 Tel.: +49/89/3209-3767 James-Franck-Str. (ehem. Bauamt) Fax.: +49/89/3209-2444 W-8046 Garching Germany email: grubi@nirvana.t30.physik.tu-muenchen.de ============================================================================== From doug@star2.cm.utexas.edu Tue Oct 13 07:52:09 1992 Date: Tue, 13 Oct 92 11:52:09 EDT From: doug@star2.cm.utexas.edu (William D Clendening) To: CHEMISTRY@ccl.net Subject: self-consistant soln of P-B eq. Hello, i'm wondering if any one has experience solving the Poisson-Boltzmann eq. using the self-consistant method presented in a paper by A. Delville (Chem. Phys. Lett. 69 p.386). i'm wondering how good the initial potential guess must be to get convergence. Thanks, Doug Clendening Univ. of Tx. at Austin doug@star2.cm.utexas.edu cmft557@emx.utexas.edu From pisdiez@quinor.edu.ar Tue Oct 13 14:17:20 1992 Date: Tue, 13 Oct 92 09:11:41 ARG From: Dr. Reinaldo Pis Diez To: chemistry@ccl.net Subject: RE: CNDO parameters for Mo Hi all, Some days ago, someone (I think her name's Laura) asked the list for CNDO parameters for Mo. There was a (negative) answer to the list, too. I've got a paper from F. Ruette et al (JACS 1989,111,40-46) con- cerning molecular analogues of surface studies. They work with Mo-CO com- plexes. They report Mo parameters of course. Further, there's another pa- per from Ruette and Ludenia on HDS catalysts where they use the CNDO me- thod, too (J Catal 1981, 67, 266). The parameters are the following: Slater exponent (I+A)/2 (eV) Beta (eV) s 1.40 3.93 7.50 p 1.40 0.71 7.50 d 2.40 4.53 11.50 Have a nice day!! Reinaldo From apa@ccadfa.cc.adfa.oz.au Wed Oct 14 20:33:35 1992 Date: Wed, 14 Oct 1992 10:33:35 +1000 From: apa@ccadfa.cc.adfa.oz.au (Alan P Arnold) To: chemistry@ccl.net Subject: Ionisation (protonation) state of an oligonucleotide I've been following the discussion about electrostatics in bio-simulations with considerable interest. We are working experimentally and modeling with a dodecanucleotide at the moment and a rather embarrassing question was asked yesterday - What is "the charge" of the oligo. The phosphate on one end is capped, leaving nominally one -ve phosphate per base so we've assumed 22-minus for the duplex. Qustion - is it "known" that the phosphate pKas are all so far below 7 (we are working in pH7 phosphate buffer) that such a -ve polyanion is completely deprotonated at pH7? Can someone provide a good "experimental" reference to this? A further (more intriguing?) question: When a highly charged cation binds in the major groove of such an oligo by predominantly electrostatic mechanism (ie no covalent binding to bases) is it possible (likely?) that the proton-tautomeric equilibrium of the bases could be perturbed - perhaps to the extent that one of the bases might be deprotonated?? Any references in this area would be greatly appreciated. ---- Alan Arnold | e-mail: apa@ccadfa.cc.adfa.oz.au Chem. Department,University College | voice : +61 6 268 8080 Australian Defence Force Academy | fax : +61 6 268 8002 CANBERRA ACT 2600 Australia |