From chemistry-request@ccl.net Tue Mar 10 02:11:10 1992 Date: Mon, 9 Mar 92 21:32:22 -0800 From: rec@snll-arpagw.llnl.GOV (Ray Cline) Subject: Request for comment To: jle@world.std.COM Status: R Joe, The response to your question regarding the continued use of potential cutoffs is system dependent, of course. Having thought a great deal about the implementation of MD and Monte Carlo on massively parallel processors (MPP), it is definitely easier to implement MD codes with infinite cutoffs. This may be the appropriate approach for potentials that are forced to use an unrealistic short-range cutoff, like most water potentials, nonlocal metal/alloy potentials, and systems that include mixed Coulombic/short-range interactions (such as many biomolecule models). In those cases when truly short-range potentials, such as 6-12 type potentials, then a different parallel implementation would result in a more efficient code and we should probably keep the cutoff. Even if you use "infinite" range potentials, you must remember that force interacts at the speed of light (3 x 10^18 angstroms/sec) and given a timestep of 10^-16 seconds would mean that you should still limit "infinite" potentials to a cutoff of a few hundred angstroms. Though this would not appear to be a problem, the capabilities of MPP machines will soon place us in the position of considering this potential constraint (and won't it be fun). Anyway, we can continue this discuss "off line" if you wish. Raymond E. Cline, Jr. Organization 8300-A Combustion Research Facility Massively Parallel Computer Research Laboratory Sandia National Laboratories Box 969 Livermore, CA 94551 phone: (510) 294-1395 email: rec@sandia.llnl.gov FAX : (510) 294-2276 From chemistry-request@ccl.net Tue Mar 10 03:59:44 1992 Date: Tue, 10 Mar 92 08:32:56 +0100 From: martin@biokth.sunet.SE (Martin Norin, Dept. Biochem., Royal Inst. Subject: Another opinion on manuscript identification. To: "chemistry@ccl.net"@kth.sunet.SE Status: R Another idea is to make the authors of a manuscript anonymous to the referee's , except for one of the editors. Martin Norin From chemistry-request@ccl.net Tue Mar 10 04:57:07 1992 Date: Tue, 10 Mar 92 00:55:11 -0800 From: ross@zeno.mmwb.ucsf.EDU (Bill Ross) To: chemistry@ccl.net Subject: mpp & nonbonded cutoffs Status: R Ray Cline mentions using a distance cutoff for vdw interactions for efficiency and for speed of light interactions (event horizon) for correctness. My question: What do people think of the utility of nonbonded cutoffs for avoiding periodic imaging in periodic boundary conditions? Another thought: Ray Cline: ... Even if you use "infinite" range potentials, you must remember that force interacts at the speed of light (3 x 10^18 angstroms/sec) and given a timestep of 10^-16 seconds would mean that you should still limit "infinite" potentials to a cutoff of a few hundred angstroms. But you could further imagine marching in waves of forces from nested few hundred angstrom shells from previous steps: a freight train leapfrog algorithm (think of the memory & communication bandwidth required). Bill Ross From chemistry-request@ccl.net Tue Mar 10 11:46:39 1992 Date: 10 Mar 92 15:09:11 EDT From: UDIM018%FRORS31.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: If it aint broken dont fix it To: chemistry@ccl.net Status: R 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 I think the current journal referee system works better than any other I can imagine and only minor modifications are necesssary. If you look around this world you'll see things a lot worse. Personally, even after nearly 20 years here in France, naturalized and as culturally adapted as one can be I still can not see substituting an anonymous evaluation with one from one can "get to". It can and does happen here with regard to promotions and various grants. The French call it "piston". However, in all cultures (we function in a trans-cultural scientific environment) there will be "clubs", networks of friends and buddies, people who know on another and other forms of tribalisms and those who have a meritorious approach will wage an unending battle against the worse features of these natural human interactions. A reviewer is always influenced by the presence of a well known author (particularly a friend) from a well known institution on a paper. A good reviewer knows he will be and attempts to play fair, particularly with regard to an young person having no recognizable place in the scientific pecking order. But having put the "knief" into the back of a personal and close friend more than once is uncomfortable and it would have affected our personal relationships if it were known that it was me who did it. I assume that editors keep list of good referees and weed out bad referees. But the current referee system is pretty much trans-cultural, one knows the rules of the game, one knows one will run into a poor referee, one knows one will have a paper unfairly refused at times. But I think the current system does promote excellence. This current system is a hard on third world research and authors and those who have problems with english. Finally, it is a game. From chemistry-request@ccl.net Tue Mar 10 12:15:47 1992 Date: Tue, 10 Mar 92 07:22:19 -0800 From: pak@cgl.ucsf.EDU (Peter Kollman) Subject: non-bonded cutoffs To: chemistry@ccl.net Status: R I wanted to add to the non-bond cutoff debate. Even though one typically uses a non-bonded cutoff that is too small, e.g. 8 angstoms, in many macromolecular simulations, it is likely better to use ewald summation than no cutoff in crystal simulations..(what does infinite cutoff really mean when one has periodic boundary conditions..it is really undefined until you define your unit cell, which you can make larger and larger)...even in solution simulations without periodic boundary conditions, with many formal charges, I would argue that infinite cutoffs might lead to artifacts because one can't run the simulations long enough to get appropriate averaging of all these formal charges to give realistic ion atmosphere effects...the cure may be worse than the disease...i do think longer than 8 angstrom cutoffs are appropriate and recommend dual cutoffs(c.f. Berendsen, van Gunsteren,Darden,Charifson) which can consider effects out to, e.g. 15 to 20 angstroms at little computational overhead...but in summary, there are many things more important in reducing simulation artefacts than switching to an infinite non-bonded cutoff--even if we could, i don't think we should. From chemistry-request@ccl.net Tue Mar 10 12:22:30 1992 Date: Tue, 10 Mar 92 09:49:05 CST From: Jan Jensen Subject: A question for Mac users To: chemistry@ccl.net Organization: North Dakota Higher Education Computer Network Status: R Fellow Netters, This is a question for all you Mac users. Is there a Mac program out there that will take a post script file and render a picture on the screen that one can cut and paste? Our graphics codes produce post script files for hard copies but it would be nice to edit the pictures on the Mac before printing. Any held will be greatly appreciated. Jan H. Jensen Dept. of Chemistry North Dakota State University Fargo, ND 58105 From chemistry-request@ccl.net Tue Mar 10 12:33:59 1992 Date: Tue, 10 Mar 92 11:05:59 EST From: "G. Ravishanker" Subject: GROMOS To: chemistry@ccl.net Status: R Hi Could someone tell how to obtain the most current GROMOS distribution? (from BIOMOS, I think) I would like to know any e-mail contact, FAX number etc. Thank you very much. Ravi From chemistry-request@ccl.net Tue Mar 10 12:34:49 1992 Date: Tue, 10 Mar 92 10:58:50 EST From: "G. Ravishanker" Subject: Commercialization of software To: chemistry@ccl.net Status: R Hi As we have seen in the past as well as present, several molecular modelling/MD packages developed in academic institutions have been commercialized in one form or other - mostly by aligning with a software company that markets the software with added functionalities and features. I am interested in knowing the views of the scientific community on several issues. I know that this discussion is likely to drain the bandwidth of the network (I hope so...), but I feel that this is an important issue. 1. What are the ethical issues on taking a product that was produced primarily by federal funding of one form or another and commercializing it? 2. Who really owns the software? The graduate students, and postdocs who really wrote the piece of code, or the professor under (or with) whom they worked, or the academic institution itself, or finally the US Govt. Agency that funded the project? 3. Since there is a considerable amount of money to be made in commercializing the software, who should and how should the money be divided? Do you go looking for all the participants of the project and geve them some sort of a share, or do you simply ignore them.... 4. If you think you have some software with commercial potential, what are all the legal implications that you need to sort out before approaching anyone? There can be several other questions along these lines and any contributions from those who have commercialized their software will especially be useful. Thank you in advance. Ravi From chemistry-request@ccl.net Tue Mar 10 12:37:52 1992 Date: Tue, 10 Mar 92 11:17:07 EST From: states@ncbi.nlm.nih.GOV (David States) Subject: Re: mpp & nonbonded cutoffs To: chemistry@ccl.net, ross@zeno.mmwb.ucsf.EDU Status: R On the general subject of cutoffs, there is a Longcharich and Brooks paper in Proteins (1989) 6:32-45 which examines the effects of non-bond cutoff distance and method in protein simulations. They argue for using cutoff of 11 A or more and either truncation or very gradual switching functions. I would argue that you don't need much longer cutoffs than that because most biological systems contain mobile counter ions. Cutting off the electrostatics effectively introduces a Debye-Huckel screening term. |> Ray Cline mentions using a distance cutoff for vdw interactions |> for efficiency and for speed of light interactions (event horizon) |> for correctness. Of course if you are going to talk about the speed of light, you need to know the index of refraction/dielectric constant of the system you are modeling. Question: Why do empirical energy calculations ignore the isotropic electronic polarizability that results in a refractive index around 1.4 (-> dielectric constant around 2)? It seems to me that if you are going to do a condensed phase simulation, you ought to include this term (or explicit atomic polarizabilities). |> What do people think of the utility of nonbonded cutoffs for avoiding |> periodic imaging in periodic boundary conditions? If you mean cutoffs/reaction fields as opposed to Ewald sums, I have never been convinced that the computational costs of doing Ewald sums correctly gave a real improvement in the simulation, but they do give you infinite range electrostatics. |> But you could further imagine marching in waves of forces from nested |> few hundred angstrom shells from previous steps: a freight train |> leapfrog algorithm (think of the memory & communication bandwidth required). What you are proposing is a bit different, but multiple timestep methods have been used to advantage in a number of molecular dynamics calculations. Instead of calculating a full atom by atom electrostatic calculation, you group the atoms into neutral multipoles and do a multipole interaction series which can be truncated at a desired accuracy and don't need to be updated as frequently as the basic MD timestep. See the original Charmm paper for the gory details. |> Bill Ross David States National Center for Biotechnology Information / National Library of Medicine From chemistry-request@ccl.net Tue Mar 10 13:02:36 1992 Date: Tue, 10 Mar 92 11:20:20 -0500 From: fredvc@esvax.dnet.dupont.COM Subject: KEEP THOSE REFEREES ANONYMOUS!! To: %chem@ccl.net Status: R I served as a journal editor for several years, and continue to referee papers for various journals. About every 5-6 years, there seems to be an upsurge in the cries for doing away with the dastardly anonymous reviewing system for papers. These calls, in my judgement are misguided. In my experience, most referees are sincere, hardworking, and trying to do the best job that they can. I cannot deny that there are a few "snakes" out there. Usually, though, an attentive editor can tell when the author/referee exchange begins to go beyond the bounds of science. My experience is that the calls for "naming the referee" tend to grow out of situations where the author has temporarily lost his/her scientific de- tachment, more often than not. He/She has such an emotional investment in the work that criticism cannot be processed effectively. It begins to approach "pathological science", much like cold fusion or polywater. A strong case against naming referees can be made, based on the "decline and fall of the letter of recommendation". As the Freedom of Information Act has removed the shield of confidentiality from school files, personnel records, etc., the letter of recommendation has generally become so bland as to be useless as originally intended. Crucial information is now transmitted by personal contact, and seldom made a part of the individual's permanent record. No editor in his/her right mind wants to have a system where the decision to reject a paper has to be made on the basis of undocumented information that cannot be passed on to the author!! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 Central Research & Development Dept. || FAX: (302) 695-9658 The Du Pont company || P. O. Box 80320 || Internet: fredvc@esvax.dnet.dupont.com Wiilmington DE 19880-0320 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@ccl.net Tue Mar 10 13:32:06 1992 Date: Tue, 10 Mar 92 11:11:51 CST From: heller@lisboa.ks.uiuc.EDU (Helmut Heller) Subject: Re: CM-5 To: wampler@bchiris.biochem.uga.EDU (John Wampler) Status: R > Does anyone have information about the suitability of > the Thinking Machines CM-5 for running computational > chemistry programs. We are interested in both quantum > chemistry and molecular mechanics based calculations > (not Monte Carlo). Does anyone have benchmarks that > would indicate the % peak performance that might be > expected for such codes. Please reply direct to > wampler@bchiris.biochem.uga.edu > Thanks in advance.. JW > The parallel molecular dynamics program named EGO is currently being ported from occam II on a Transputer system to C to run on the CM5. The port is almost completed and first benchmarks are to be expected soon. Nevertheless one has to keep in mind that without vector units one should not expect too much speed. Servus, Helmut (W9/DH0MAD) _________________________________________________ heller@lisboa.ks.uiuc.edu "Knowledge must be gathered and cannot be given" FAX: (217)244-1080 ZEN, one of BLAKES7 Phone: (217)244-6914, ------------------------------------------------- Helmut Heller, University of Illinois at Urbana-Champaign, Beckman Institute Theoretical Biophysics Group, Room 3143, MC 251 405 N. Mathews Ave., Urbana, IL 61801, U.S.A. From chemistry-request@ccl.net Tue Mar 10 13:33:24 1992 Date: Tue, 10 Mar 92 08:50:15 -0800 From: rec@snll-arpagw.llnl.GOV (Ray Cline) Subject: mpp & nonbonded cutoffs To: ross@zeno.mmwb.ucsf.EDU Status: R Bill Ross mentions: > But you could further imagine marching in waves of forces from nested > few hundred angstrom shells from previous steps: a freight train > leapfrog algorithm (think of the memory & communication bandwidth required). When using a short-range cutoff it is possible to develop a systolic type algorithm that pipelines timesteps as well as parallelizing the force/potential calculations. I originally thought about this a couple of years ago to increase sample sizes by doing out-of-core stuff. The interesting thing about this technique is that you can replace the disk with another computer and therefore would be useful for distributed computing and/or multiple mpp machines. You can even do this with periodic boundary conditions! (Though personally I believe that one of the major advantages to larger scale simulations would be to remove the need for periodic boundaries) Again, I would be interested in discussing these ideas with all others interested (perhaps point-topoint e-mail would be better, though if the general net is interested I'll continue to respond). Raymond E. Cline, Jr. Organization 8300-A Combustion Research Facility Massively Parallel Computer Research Laboratory Sandia National Laboratories Box 969 Livermore, CA 94551 phone: (510) 294-1395 email: rec@sandia.llnl.gov FAX : (510) 294-2276 From chemistry-request@ccl.net Tue Mar 10 13:33:24 1992 Date: Tue, 10 Mar 92 08:50:15 -0800 From: rec@snll-arpagw.llnl.GOV (Ray Cline) Subject: mpp & nonbonded cutoffs To: ross@zeno.mmwb.ucsf.EDU Status: R Bill Ross mentions: > But you could further imagine marching in waves of forces from nested > few hundred angstrom shells from previous steps: a freight train > leapfrog algorithm (think of the memory & communication bandwidth required). When using a short-range cutoff it is possible to develop a systolic type algorithm that pipelines timesteps as well as parallelizing the force/potential calculations. I originally thought about this a couple of years ago to increase sample sizes by doing out-of-core stuff. The interesting thing about this technique is that you can replace the disk with another computer and therefore would be useful for distributed computing and/or multiple mpp machines. You can even do this with periodic boundary conditions! (Though personally I believe that one of the major advantages to larger scale simulations would be to remove the need for periodic boundaries) Again, I would be interested in discussing these ideas with all others interested (perhaps point-topoint e-mail would be better, though if the general net is interested I'll continue to respond). Raymond E. Cline, Jr. Organization 8300-A Combustion Research Facility Massively Parallel Computer Research Laboratory Sandia National Laboratories Box 969 Livermore, CA 94551 phone: (510) 294-1395 email: rec@sandia.llnl.gov FAX : (510) 294-2276 From chemistry-request@ccl.net Tue Mar 10 14:11:06 1992 Date: Tue, 10 Mar 92 12:28:35 -0500 From: radomski@mond1.ccrc.uga.EDU Subject: Re: Request for comment [on MD & MPP] To: chemistry@ccl.net Status: R Ray Cline wrote: >Anyway, we can continue this discuss "off line" if you wish. PLEASE DON'T if you could afford to do it "on line". This is very interesting and "vital" discussion. Regards, Jan. -------------------------------------------------- Jan P. Radomski Complex Carbohydr. Res. Center, Univ. of Georgia, 220 Riverbend Rd., Athens, 30602 GA. -------------------------------------------------- From reg@chem.UCSD.EDU Tue Mar 10 14:52:26 1992 From: reg@chem.UCSD.EDU (Richard E. Gillilan) Subject: Re: A question for Mac users To: chemistry-request@ccl.net (Jan Jensen) Date: Tue, 10 Mar 92 11:51:33 PST Status: R > > > Fellow Netters, > > This is a question for all you Mac users. Is there a Mac program out > there that will take a post script file and render a picture on the > screen that one can cut and paste? Our graphics codes produce post > script files for hard copies but it would be nice to edit the pictures on the > Mac before printing. Any held will be greatly appreciated. > > Jan H. Jensen > Dept. of Chemistry > North Dakota State University > Fargo, ND 58105 > To public domain suite of codes called pbmplus contains a program called psidtopgm (postscript image data to pgm format). pbmplus also contains utilites to convert from pgm to just about anything. A number of MAC programs (like canvas) will read in TIFF and other similar formats. I can't remember the anon ftp site offhand, but I dig it up if you're interested. Ps. I haven't actually tried this but I have done it the other way around. pgmtops produces surprisingly nice BW laserprinter images from raster files. ---------------------------------- Richard E. Gillilan Postgraduate Research Chemist, UCSD reg@sdchemw2.ucsd.edu From chemistry-request@ccl.net Tue Mar 10 15:10:07 1992 Date: Tue, 10 Mar 92 10:43:13 -0800 From: ross@zeno.mmwb.ucsf.EDU (Bill Ross) Subject: commercialization To: chemistry@ccl.net Status: R I think that codes developed under govt funding should be made available for distribution/maintenance costs. I haven't devoted much thought to the ideal legal permissions to grant. If subsequent commercialization adds value, the precommercial version should remain available on the same terms. This "nothing for anyone" policy is the closest I can imagine to fair for myriad unsung contributors as well as being the appropriate consequence of public funding (assigning credit is another side of the coin). Once a transition to commercial code has occurred, further deveopments transpire under known ground rules and participants can negotiate a slice of the pie. Hopefully funding agencies factor in the degree of commercialization in allocating funds. Bill Ross From chemistry-request@ccl.net Tue Mar 10 15:36:00 1992 Date: Tue, 10 Mar 1992 14:02:47 EST From: Bill Winter To: chemistry@ccl.net Status: R Here is the final program for the Tutorial/Symposium on Static and Dynamic Modeling of Polysaccharides and Carbohydrates to be held at the ACS meeting in SanFrancisco April 5-10 =========================cut here========================================== PROGRAM: Static and Dynamic Modeling of Polysaccharides and Carbohydrates Spring Meeting of the American Chemical Society, San Francisco, CA April 5-10, 1992 Sponsor: Cellulose, Paper and Textile Division Co-Sponsor: Carbohydrate Division of the American Chemical Society Meetings will be in the Exhibition Hall Organizer: W. T. Winter, Chemistry Department, SUNY-ESF. Tutorial Session Session 1: Sunday April 5, 1992 AM - Tutorial on Static and Dynamic Modeling Presiding: W.T. Winter 8:30 An Overview of Computational Chemistry. A. Sarko 9:25 Quantum Chemical Applications to Carbohydrates and Their Analogs. Y. -J. Zheng and K. M. Merz Jr. (coffee break 10:20-10:35) 10:35 Molecular Mechanics Modeling of Oligo- and Polysaccharides. S. Perez 11:30 Force Field Development for Carbohydrates and Polysaccharides. J. Brady (lunch 12:25 - 2:00) Session 2: Sunday April 5, 1992 PM - Tutorial on Static and Dynamic Modeling Presiding:A. Sarko 2:00 Applications of Molecular Dynamic to Carbohydrate Containing Molecules. B. Hardy 2:55 Conformational Analysis of Polysaccharides Using NMR and Potential Energy Calculations. J.-R. Brisson (coffee break 3:50 - 4:05) 4:05 Diffraction Data Restraints on Polysaccharide Modeling. W. T. Winter 5:00 Ab initio Molecular Orbital Calculations on 2- Deoxy- beta - D - glycero -tetro-furanose:Effect of Glycosidation and C-O Torsion Angles on Ring Structure and Conformation. A.S. Serianni Session 3: Monday April 6, 1992 AM - Symposium on Static and Dynamic Modeling of Polysaccharides and Carbohydrates. Presiding: B. Hardy 8:30 Conformational Features of Carrabiose. A. DiBlas, R. Urbani, A. Cesaro. 8:55 Conformational Analysis of the Anomeric Forms of Kojibiose, Nige Using MM3. M. K. Dowd, J. Zeng, A. D. French, P. J. Reilly. 9:20 Molecular Dynamics Simulations of Lewis Blood Groups Oligosaccharides. C. A. Bush, C. Mukhopadhyay. 9:45 Properties of Carbon-Centered Radicals of Deoxyribose: Quantum Chemistry Simulations of Hydrogen Abstraction by OH Radicals. R. Osman, L. Pardo, K. Miaskiewicz. 10:10 - 10:25 coffee break Presiding: A. Sarko 10:25 Conformational Behaviour of Thio-Sugars in Solution. K. Mazeau, F. Taravel, I. Tvaroska. 10:50 J. Carver - Paper Withdrawn 11:15 A Molecular Dynamics Simulation and Nuclear Overhauser Effect NMR Spectroscopy Study of a -L-Rhap(1 - 2)-a -L-Rhap - (1 - OMe) W. Egan, G. Widmalm. 11:40 Modeling the Calicheamicin g1I Oligosaccharide. D. M. Gange, S. Walker, D. Kahne. 12:05-1:30 lunch Session 4: Monday April 6, 1992 PM - Symposium on Static and Dynamic Modeling of Polysaccharides and Carbohydrates. Presiding: A. D. French 1:30 Calculation of Ensemble- Averaged Molecular Properties of Oligosac- charides for Comparison with Experiment. B. J. Hardy 1:55 Exploring The Effects of Sidechain-Backbone Interactions in Bacterial and Other Branched Polysaccharides. B. T. Stokke, T. A. Talashek, D. A. Brant 2:20 Conformational Features of Pyruvyl-Substituents in Microbial Polysaccharides. S. Miertus, L. Navarini, A. Cesaro. 2:45 Molecular Carbohydrate Structure at Membrane Surfaces Using Empirical Force Fields and NMR Data. J. H. Prestegard. 3:10 - 3:25 coffee break 3:25 Using Optical Rotation to Probe Carbohydrate Potential Energy Surfaces. E.S. Stevens 3:50 An Improved Version of the Random Molecular Mechanics (RAMM2) Program: Conformational Properties of the (1-2) and (1-3) Linkages in Disaccharides and Vicinally Glycosylated Trisaccharides. T. Kozar, J. Dabrowski 4:15 Serious Computer Modeling of Carbohydrates on a PC? A.D. French 4:40 Experiences with Alchemy II/ MM2 Based Oligo- and Polysaccharide Modeling. B. Tinland, W. T. Winter 5:05 Modeling Flexible Fructofuranose Oligomers. A.L. Waterhouse, J. Liu Questions or further info?? Contact me by these methods... William T. Winter, Polymer Structure and Dynamics Group 315 Baker Lab, SUNY-ESF, Syracuse, NY 13210-2786, USA Internet: wtwinter@suvm.acs.syr.edu ; Bitnet: wtwinter@suvm Phone: (315)470-6876; FAX: (315)470-6512