From 9702029k@lv.levels.unisa.edu.au Thu Aug 6 03:15:23 1998 Received: from bROLga.Levels.UniSA.Edu.Au (SYSTEM@Brolga.levels.unisa.edu.au [130.220.16.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA17017 Thu, 6 Aug 1998 03:15:21 -0400 (EDT) Received: from XIY205359.Levels.UniSA.Edu.Au ("port 1040"@XIY205359.Levels.UniSA.Edu.Au) by Levels.UniSA.Edu.Au (PMDF V5.1-10 #27872) with SMTP id <01J0AGI7H8V28WW389@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Thu, 6 Aug 1998 16:45:15 +0930 Received: by XIY205359.Levels.UniSA.Edu.Au with Microsoft Mail id <01BDC15A.300519E0@XIY205359.Levels.UniSA.Edu.Au>; Thu, 06 Aug 1998 16:49:33 +0930 Date: Thu, 06 Aug 1998 16:49:31 +0930 From: Josh Bowden <9702029k@lv.levels.unisa.edu.au> Subject: Summary : RAID 0 for speed? To: "'chemistry@www.ccl.net'" Message-id: <01BDC15A.300519E0@XIY205359.Levels.UniSA.Edu.Au> MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id DAA17017 Summary of responses regarding RAID 0, thanks to you who replied. I am wondering now is NTFS supported by Gaussian98 ? Q1: I am wondering if anybody has experience with RAID 0 setup for workstations running ab-initio programs. I would think that this would be a v.good way to increase disk access speed and a good way to increase disk storage space. Does RAID 0 increase integral file R/W access and therefore increase computational speed? or are other areas the bottleneck in a computer+ab-initio program? Is anyone usinig IDE HD RAID cards, such as those from Promise Tech. and have you found that these increase computational performance? A1: With respect to SCSI RAID 0 the answer is a big yes, yes. However if you are using the HyperCube or Gaussian products with NT as the OS then the answer is maybe. Both companies have limited the file size to 2GB which they say is based on FAT 32. I have communicated with them many times about implementing NTFS. It is a simple procedure and both companies have indicated that they will support the NTFS file structure in their next release. For FAT the max file size is 2^32 bytes (4.3 GB). For NTFS, the max is 2^64 bytes (1.8 x 10^10 GB). I don't think this is much of limitation. Laurence Q2: Has anyone tried the RAID 0 setup on NT (striped sets) (ie software controled RAID) and does it make any difference to disk access times/computational speed? A2: I have tried it and it works, but I have not compared the performance to a non-striped set. A manual from Adaptec cites about 15% performance gain, if the drives are on separate SCSI channels. I am not sure what the gain would be on separate EIDE channels. Bottom line: if you have two similar drives and want one file system - always stripe. Slawomir Janicki slawek@alchmist.scs.uiuc.edu Thanks again Josh Josh Bowden University of South Australia Ian Wark Research Institute 9702029k@lv.levels.unisa.edu.au From g.germano@bristol.ac.uk Thu Aug 6 06:59:08 1998 Received: from cockatoo.phy.bris.ac.uk (cockatoo.phy.bris.ac.uk [137.222.30.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA17454 Thu, 6 Aug 1998 06:59:07 -0400 (EDT) Received: by cockatoo.phy.bris.ac.uk id AA08725; Thu, 6 Aug 1998 11:58:25 -0400 Date: Thu, 6 Aug 1998 11:58:25 -0400 (EDT) From: Guido Germano X-Sender: guido@cockatoo.phy.bris.ac.uk Reply-To: Guido Germano To: Timm Lankau Cc: chemistry@www.ccl.net Subject: Re: G94 cube file to gnuplot (3D data) Message-Id: Organization: Department of Physics - University of Bristol Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I am looking for a simple program / shell script, which converts density > data from a G94 cube file to a data file suitable for gnuplot to > generate a 3D surface plotable with 'splot'. Write this into a file called e.g. grid.awk, setting N to the appropriate value: BEGIN {N = 100} NF == 1 {print $0; i++} i == N {print ""; i = 0} Then issue the command (I suppose you are working under Unix) awk -f grid.awk g94_file.grid > gnu_file.grid You can also avoid writing gnu_file.grid to disk, issuing directly from the gnuplot prompt the command: splot '< awk "BEGIN {N = 100}; NF == 1 {print $0; i++}; i == N {print \"\"; i = 0} g94_file.grid' notitle w l You can write the above line into a file called e.g. splot.gnu and then issue from the gnuplot prompt: load 'splot.gnu' Freundliche Gruesse Dr. Guido Germano Research Assistant in Theoretical Physics, University of Bristol, England Tel. +44-117-928 8755, http://www.phy.bris.ac.uk/staff/germano_g.html From destack@unomaha.edu Thu Aug 6 09:38:24 1998 Received: from s-cwis.unomaha.edu (s-cwis.unomaha.edu [137.48.1.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA18536 Thu, 6 Aug 1998 09:38:23 -0400 (EDT) Received: from cas.unomaha.edu (cas.unomaha.edu [137.48.34.40]) by s-cwis.unomaha.edu (8.8.5/8.8.5) with ESMTP id IAA09389 for ; Thu, 6 Aug 1998 08:33:59 -0500 (CDT) Received: from CAS/MAILQUEUE by cas.unomaha.edu (Mercury 1.21); 6 Aug 98 08:38:24 -600 Received: from MAILQUEUE by CAS (Mercury 1.21); 6 Aug 98 08:38:12 -600 Received: from zinc.unomaha.edu by cas.unomaha.edu (Mercury 1.21); 6 Aug 98 08:38:03 -600 Received: by zinc.unomaha.edu with Microsoft Mail id <01BDC116.1F6EAC70@zinc.unomaha.edu>; Thu, 6 Aug 1998 08:42:19 -0500 Message-ID: <01BDC116.1F6EAC70@zinc.unomaha.edu> From: "Douglas E. Stack" To: "'CCL'" Subject: Syntax for Cube option in Gaussian94 Date: Thu, 6 Aug 1998 08:42:18 -0500 Return-Receipt-To: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id JAA18536 I'm having problems using the cube properties keyword in Gaussian94. I'd like to evaluate both the HOMO and the LUMO molecular orbitals. The manual is not too clear on this keyword. It states that the orbitals option should be followed by the cube filename immediately followed by a list of orbitals. I've try the following with no luck. Cube=orbitals filename HOMO LUMO Cube=(orbitals,filename, HOMO,LUMO) Cube=orbitals filename HOMO LUMO Cube=orbitals filename HOMO LUMO Can any help me with the correct syntax for this keyword, Thanks! Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From chem@feldmann.nist.gov Thu Aug 6 10:39:01 1998 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA19112 Thu, 6 Aug 1998 10:39:00 -0400 (EDT) From: chem@feldmann.nist.gov Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.8.8/8.8.8) with SMTP id KAA02057 for ; Thu, 6 Aug 1998 10:37:46 -0400 (EDT) Received: from localhost by feldmann.nist.gov (SMI-8.6/SMI-SVR4) id KAA02286; Thu, 6 Aug 1998 10:34:20 -0400 Date: Thu, 6 Aug 1998 10:34:19 -0400 (EDT) To: CHEMISTRY@www.ccl.net Subject: ChemInt 98 - Poster Session Added Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A poster session has been added to the Chemistry and the Internet Conference (ChemInt98). Posters will be presented both Sunday and Monday after lunch. There will be just one poster session - all posters will be available at both times. Contributors who wish to show a poster at the meeting should email the title, the authors names, their affiliation and an abstract to Steven Bachrach, smb@smb.chem.niu.edu, prior to August 31, 1998. Authors should also indicate what medium they will be using for their poster, i.e. paper, computer, etc. The conference will be held from Sep. 12-15, 1998 in Irvine CA. For complete information, see http://www.ijc.com/ci1/ Steve Bachrach -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From chem@feldmann.nist.gov Thu Aug 6 10:39:21 1998 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA19124 Thu, 6 Aug 1998 10:39:21 -0400 (EDT) From: chem@feldmann.nist.gov Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.8.8/8.8.8) with SMTP id KAA02149 for ; Thu, 6 Aug 1998 10:38:06 -0400 (EDT) Received: from localhost by feldmann.nist.gov (SMI-8.6/SMI-SVR4) id KAA02289; Thu, 6 Aug 1998 10:34:40 -0400 Date: Thu, 6 Aug 1998 10:34:40 -0400 (EDT) To: CHEMISTRY@www.ccl.net Subject: ChemInt'98 conference Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII <<<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>> ChemInt'98 - Chemistry and the Internet - will be held in Irvine, CA on September 12-15, 1998. For details, please look at the url: http://www.ijc.com/ci1/ <<<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>> This conference will look into the current and future technologies and developments for chemistry using the internet. This meeting will gather together the leaders and innovators in developing Internet resources for chemists, leading to discussions of what future innovations and direction will bring to chemists. Chemists who use the Internet on a regular basis, webmasters and web developers for chemistry sites, and web publishers will benefit greatly from this conference. In addition, working chemists who want to learn from leaders in this high growth and high visibility area what the current and future value of the Internet will also find the conference of great value. Technical Sponsors: ACS CINF Division ACS COMP Division The Chemical Structure Association (CSA) Special Libraries Association (SLA) Chemistry Division Japan Asscoiation for International Chemical Information Speakers: Wendy Warr, Wendy Warr & Associates Barry Hardy, VEI Matt Hahn, MSI Mark J. Winter, University of Sheffield Henry Rzepa, Imperial College, London Joost Kircz, Elsevier Science, The Netherlands Michael Newman, Stanford University Peter Murray Rust, University of Nottingham Dave Weininger, Daylight Chemical Information Systems Nestor J. Zaluzec, Argonne National Labs In addition there are 10 contributed talks. See the program for details (www.ijc.com/ci1/) NEW (7/23/98): Poster papers are now being accepted for the conference! Computer facilities and internect access will be available at the meeting. 11 companies will also be exhibiting their chemistry/internet products at the meeting. From dons@hamilton.math.missouri.edu Tue Aug 4 15:01:30 1998 Received: from math.missouri.edu (math.missouri.edu [128.206.72.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA06090 Tue, 4 Aug 1998 15:01:29 -0400 (EDT) Received: from hamilton.math.missouri.edu by math.missouri.edu via ESMTP (940816.SGI.8.6.9/940406.SGI) for <@math.missouri.edu:chemistry@www.ccl.net> id OAA05238; Tue, 4 Aug 1998 14:01:31 -0500 Received: by hamilton.math.missouri.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id NAA27849; Tue, 4 Aug 1998 13:28:37 -0500 From: "Don Steiger" Message-Id: <9808041328.ZM27847@hamilton.math.missouri.edu> Date: Tue, 4 Aug 1998 13:28:35 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Drug design - summary. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Below is a summary of the replies to a question I recently posted. I would like to thank everybody who replied to the question. First the question. > I am a math graduate student and working with one of the theoretical chemist at > the university here I developed a multipole algorithm for calculating coulomb > interactions. With some modifications, this method can be used as a rapid > screening procedure for the electrostatic version of the docking problem. > The chemist that I am working with feels that this is a very important problem > in the area of drug design and that I should pursue it further. In helping me > to decide if I should pursue this, I was wondering if someone could briefly > summarize the state of the art in this field. The reply summary follows. > Hierarchical multpole methods are very usefull mathematical > tools in chemsitry. See my page for papers with bibliography > on this topic. > > On the other hand, attempting to fit or parameterize chemical > interactions with multipoles (or other functions) is an art, not a > science, as there are an infinite number of posibilities. My two > cents is to focous on mathematical tools, and to avoid at all > costs anything that looks like a parameterization. > > Cheers, Matt > > +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > Matt Challacombe > Los Alamos National Laboratory http://www.t12.lanl.gov/~mchalla/ > Theoretical Division email: mchalla@t12.lanl.gov > Group T-12, Mail Stop B268 phone: (505) 665-5905 > Los Alamos, New Mexico 87545 fax: (505) 665-3909 ______________________________________________________________________________ I am somewhat familiar with the work of the above individual. Two very interesting and novel papers of his are the following. 1) Fast assembly of the Coulomb matrix: A quantum chemical tree code. J. Chem. Phys. 104(12) pages 4685-4698. 2) Linear scaling computation of the Fock matrix. J. Chem. Phys. 106(13) pages 5526-5536. Don _____________________________________________________________________________________________________________________________ > The difficulty here, as I understand it, is that multipole methods > are useful only in the "far field" case, while it is nearby interactions > that predominate in protein/ligand interactions. I looked into > multipole methods for a slightly different, but related, purpose > some years back and decided that it wasn't worth it. But don't let > my decision for a somewhat different problem and a less-than-perfect > understanding of multipole expansions discourage you from looking into > the problem more deeply yourself. Just make sure that the part of the total > calculation that you want to speed up is a sufficiently large part of > the total calculation that it makes a difference. Remember that a > 90% speed-up of 10% of the calculation is only a 9% improvement overall. > > > regards, > > Ethan A Merritt > > ----------------------------------------------------------------- > Dept of Biological Structure K428b Health Sciences > University of Washington SM-20 (206)543-1421 > Seattle, WA 98195-7742 merritt@u.washington.edu Comment. Multipole expansions have decent convergence only in the far field case. However, I think this problem can be ameliorated with a couple of tricks. The first is to fragment the molecules and compute the multipole moments for each of the fragments. The second trick would be to use non-linear convergence acceleration methods on the multipole expansion. This idea has been tried on a spherical harmonic multipole expansion by H.H.H. Homeier in a paper recently published in the Internet Journal of Chemistry; http://www.ijc.com/articles/1998v1/28. What I suspect to be the most difficult problem to work around are the induced effects. Don ________________________________________________________________________________ > Greengard-Rokhlin algorithm. Leslie Greengard is at Yale. > I don't know who has implemented this for finding molecular > energies. Use Science Citation Index to find out. Can > you treat molecular models in solution, with one > dielectric constant inside the molecule, and a second, > in general different, dielectric constant outside the > molecule? I have a fast diffusion method for solving these problems. > We are using it to calculate solvation energies of macromolecules. > > > Best, > > Jim Given > > Center for Advanced Research in Biotechnology _______________________________________________________________________________ > While purely electrostatic interaction potentials were developed and > tried a few decades ago, they remain a very important part of > computational chemistry. At present, most people do not use multipolar > representations for electrostatic interations (they stick with monomers > alone or use bond dipoles) since the computational time for multipolar > interaction calculations is significantly greater. Don Williams > (Kentucky, I think) has some code which will fit electrostatic > potentials to a set of multipoles, of both atom and bond centered > character. I believe that this code can also be used to compute and > export potentials using the derived multipoles. There are a number of > other groups who have worked in this area, so please do not assume that > this posting is comprehensive. Price, Stone and our own group > (Breneman) have also worked in this area. Earlier workers are Ritchie > and Hirschfeld. There is a rich literature in this area, but there is > always room for good ideas. > > Prof Curt Breneman > RPI Chemistry Department ________________________________________________________________________________ > That work sounds very interesting and I would like to hear about any useful > replies you get please. My colleague, Frank Burden (Chemistry Department > Monash University) have been working on molecular multipoles for screening > applications for some time. We are basically improving the methods > developed by Silverman and Platt (Platt, D.E.; Silverman, B.D. J. > Computat. Chem. (1996), 17, 358-66; > Silverman, B.D; Platt, D.R. J. Med. Chem. (1996) 39, 2129-40). The > critical question for drug design is how you define your axis system for > the electric multipoles with respect to the inertial axes. If this can be > done correctly, the so-called 'alignment problem' (the need to superimpose > molecules which at act at the same receptor in a consistent way) can be > eliminated. We do not agree with how S&P have defined theirs by feel they > were on the right track. We have also added steric/inertial multipoles and > , in collaboration with Glen Kellogg at Virginia Commonwealth University, > have included 'hydropoles' (essentially expansions of the lipophilic > properties of drug molecules). > > We would be interested in hearing more about your work. Can you send us > any papers, reports, theses etc on what you have achieved? > > Cheers, > > Dave > > Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au > Senior Principal Research Scientist Voice: 61-3-9545-2477 > CSIRO Molecular Science Fax: 61-3-9545-2446 > Private Bag 10,Clayton South MDC 3169 http://www.csiro.au > Australia http://www.molsci.csiro.au > > _______________________________________________________________________________ > Check out papers by > Greengard and Rokhlin, > S.Lustig and N.J.Wagner et.al. > sorry don't have them handy, > these are all quite recent publications, last maybe 4-5 years, > I am sure you'll find it in the database, > > Hope this helps, > Mike > > ------------------------------------------------------------------------------- > Michael J. Kotelyanskii Phone (814) 863 43 81 > Polymer Science Program FAX (814) 865 29 17 > Department of Materials Science and > Engineering kotelyan@plmsc.psu.edu > Pennsylvania State University http://www.plmsc.psu.edu/~kotelyan > University Park, PA 16802, USA ________________________________________________________________________________ > Yes, treating correctly Coulomb interactions in molecular simulations > (without using a cutoff in the list of interacting centers) is indeed an > important topic. The contest seems to have been won by smooth particle > mesh Ewald sums (SPME), which scales as O(N) like the fast multipole > technique, but with a much smaller costant factor, as I am said: see > T.A. Darden, D.M. York, L.G. Pedersen, J. Chem. Phys., 98, 10089 (1993); > U. Essmann, L. Perera, M. Berkowitz, T. Darden, H. Lee, L.G. Pedersen, > J. Chem. Phys., 103, 8577 (1995); P. Procacci and M. Marchi, J. Chem. > Phys., 104, 3003-3012 (1996); P. Procacci, T. Darden, M. Marchi, > J. Phys. Chem., 100, 10464-10468 (1996). > > Two references for the fast multipole method, which I admit to have > never read though, are K.E. Schmidt, M.A. Lee, J.Stat.Phys. 1223-1235 > (1991) and J. Shimada, H. Kaneko, T. Takada, J. Comp. Chem. 15, 28 > (1994). See also the book D.Frenkel, B.Smit, Understanding Molecular > Simulation, Academic Press (1996). > > It's not clear to me, however, if high accuracy and periodic boundary > conditions are needed in docking problems as well as in molecular > dynamics simulations. If they aren't, maybe the fast multipole method > which was originally devised for a cluster of ions is indeed a better > choice than SPME. > > Regards > > Dr. Guido Germano > > Research Assistant in Theoretical Physics, University of Bristol, England > Tel. +44-117-928 8755, http://www.phy.bris.ac.uk/staff/germano_g.html > ________________________________________________________________________________ > There is an abundance of reviews on drug design. Look at the book series, > Reviews in Computational Chemistry, edited by Lipkowitz and myself. > Particularly Vol. 5 (1994) and Vol. 11 (1997). These books will probably be > in your chemistry department library. Also, take a look at the May 1998 issue > of CHEMTECH magazine, p.19. Again it should be in your chemistry department > library. > > Don > Donald B. Boyd, Ph.D. > Editor, Journal of Molecular Graphics and Modelling > Department of Chemistry > Indiana University-Purdue University at Indianapolis > 402 North Blackford Street > Indianapolis, Indiana 46202-3274, U.S.A. > E-mail boyd@chem.iupui.edu ________________________________________________________________________________ > I suggest that you look at papers by S L Price (University College > London) to see applications of multipole calculations in molecular > modelling. However her work may not be directly applicable to > docking calculations: I think she is mainly interested in small- > molecule crystallographic modelling issues. Certainly multipole > calculations are an important technique in that area (although > they are rarely used in practice because the major modelling > software packages cannot handle them at present). I don't know > anything about docking myself so I cannot comment on how useful > they would be in docking calculations. > > -- > John Osborn > University of Bradford, UK. > Email j.c.osborn@bradford.ac.uk -- Don Steiger dons@hamilton.math.missouri.edu From dons@hamilton.math.missouri.edu Tue Aug 4 15:01:30 1998 Received: from math.missouri.edu (math.missouri.edu [128.206.72.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA06090 Tue, 4 Aug 1998 15:01:29 -0400 (EDT) Received: from hamilton.math.missouri.edu by math.missouri.edu via ESMTP (940816.SGI.8.6.9/940406.SGI) for <@math.missouri.edu:chemistry@www.ccl.net> id OAA05238; Tue, 4 Aug 1998 14:01:31 -0500 Received: by hamilton.math.missouri.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id NAA27849; Tue, 4 Aug 1998 13:28:37 -0500 From: "Don Steiger" Message-Id: <9808041328.ZM27847@hamilton.math.missouri.edu> Date: Tue, 4 Aug 1998 13:28:35 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Drug design - summary. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Status: RO Content-Length: 11442 Below is a summary of the replies to a question I recently posted. I would like to thank everybody who replied to the question. First the question. > I am a math graduate student and working with one of the theoretical chemist at > the university here I developed a multipole algorithm for calculating coulomb > interactions. With some modifications, this method can be used as a rapid > screening procedure for the electrostatic version of the docking problem. > The chemist that I am working with feels that this is a very important problem > in the area of drug design and that I should pursue it further. In helping me > to decide if I should pursue this, I was wondering if someone could briefly > summarize the state of the art in this field. The reply summary follows. > Hierarchical multpole methods are very usefull mathematical > tools in chemsitry. See my page for papers with bibliography > on this topic. > > On the other hand, attempting to fit or parameterize chemical > interactions with multipoles (or other functions) is an art, not a > science, as there are an infinite number of posibilities. My two > cents is to focous on mathematical tools, and to avoid at all > costs anything that looks like a parameterization. > > Cheers, Matt > > +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > Matt Challacombe > Los Alamos National Laboratory http://www.t12.lanl.gov/~mchalla/ > Theoretical Division email: mchalla@t12.lanl.gov > Group T-12, Mail Stop B268 phone: (505) 665-5905 > Los Alamos, New Mexico 87545 fax: (505) 665-3909 ______________________________________________________________________________ I am somewhat familiar with the work of the above individual. Two very interesting and novel papers of his are the following. 1) Fast assembly of the Coulomb matrix: A quantum chemical tree code. J. Chem. Phys. 104(12) pages 4685-4698. 2) Linear scaling computation of the Fock matrix. J. Chem. Phys. 106(13) pages 5526-5536. Don _____________________________________________________________________________________________________________________________ > The difficulty here, as I understand it, is that multipole methods > are useful only in the "far field" case, while it is nearby interactions > that predominate in protein/ligand interactions. I looked into > multipole methods for a slightly different, but related, purpose > some years back and decided that it wasn't worth it. But don't let > my decision for a somewhat different problem and a less-than-perfect > understanding of multipole expansions discourage you from looking into > the problem more deeply yourself. Just make sure that the part of the total > calculation that you want to speed up is a sufficiently large part of > the total calculation that it makes a difference. Remember that a > 90% speed-up of 10% of the calculation is only a 9% improvement overall. > > > regards, > > Ethan A Merritt > > ----------------------------------------------------------------- > Dept of Biological Structure K428b Health Sciences > University of Washington SM-20 (206)543-1421 > Seattle, WA 98195-7742 merritt@u.washington.edu Comment. Multipole expansions have decent convergence only in the far field case. However, I think this problem can be ameliorated with a couple of tricks. The first is to fragment the molecules and compute the multipole moments for each of the fragments. The second trick would be to use non-linear convergence acceleration methods on the multipole expansion. This idea has been tried on a spherical harmonic multipole expansion by H.H.H. Homeier in a paper recently published in the Internet Journal of Chemistry; http://www.ijc.com/articles/1998v1/28. What I suspect to be the most difficult problem to work around are the induced effects. Don ________________________________________________________________________________ > Greengard-Rokhlin algorithm. Leslie Greengard is at Yale. > I don't know who has implemented this for finding molecular > energies. Use Science Citation Index to find out. Can > you treat molecular models in solution, with one > dielectric constant inside the molecule, and a second, > in general different, dielectric constant outside the > molecule? I have a fast diffusion method for solving these problems. > We are using it to calculate solvation energies of macromolecules. > > > Best, > > Jim Given > > Center for Advanced Research in Biotechnology _______________________________________________________________________________ > While purely electrostatic interaction potentials were developed and > tried a few decades ago, they remain a very important part of > computational chemistry. At present, most people do not use multipolar > representations for electrostatic interations (they stick with monomers > alone or use bond dipoles) since the computational time for multipolar > interaction calculations is significantly greater. Don Williams > (Kentucky, I think) has some code which will fit electrostatic > potentials to a set of multipoles, of both atom and bond centered > character. I believe that this code can also be used to compute and > export potentials using the derived multipoles. There are a number of > other groups who have worked in this area, so please do not assume that > this posting is comprehensive. Price, Stone and our own group > (Breneman) have also worked in this area. Earlier workers are Ritchie > and Hirschfeld. There is a rich literature in this area, but there is > always room for good ideas. > > Prof Curt Breneman > RPI Chemistry Department ________________________________________________________________________________ > That work sounds very interesting and I would like to hear about any useful > replies you get please. My colleague, Frank Burden (Chemistry Department > Monash University) have been working on molecular multipoles for screening > applications for some time. We are basically improving the methods > developed by Silverman and Platt (Platt, D.E.; Silverman, B.D. J. > Computat. Chem. (1996), 17, 358-66; > Silverman, B.D; Platt, D.R. J. Med. Chem. (1996) 39, 2129-40). The > critical question for drug design is how you define your axis system for > the electric multipoles with respect to the inertial axes. If this can be > done correctly, the so-called 'alignment problem' (the need to superimpose > molecules which at act at the same receptor in a consistent way) can be > eliminated. We do not agree with how S&P have defined theirs by feel they > were on the right track. We have also added steric/inertial multipoles and > , in collaboration with Glen Kellogg at Virginia Commonwealth University, > have included 'hydropoles' (essentially expansions of the lipophilic > properties of drug molecules). > > We would be interested in hearing more about your work. Can you send us > any papers, reports, theses etc on what you have achieved? > > Cheers, > > Dave > > Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au > Senior Principal Research Scientist Voice: 61-3-9545-2477 > CSIRO Molecular Science Fax: 61-3-9545-2446 > Private Bag 10,Clayton South MDC 3169 http://www.csiro.au > Australia http://www.molsci.csiro.au > > _______________________________________________________________________________ > Check out papers by > Greengard and Rokhlin, > S.Lustig and N.J.Wagner et.al. > sorry don't have them handy, > these are all quite recent publications, last maybe 4-5 years, > I am sure you'll find it in the database, > > Hope this helps, > Mike > > ------------------------------------------------------------------------------- > Michael J. Kotelyanskii Phone (814) 863 43 81 > Polymer Science Program FAX (814) 865 29 17 > Department of Materials Science and > Engineering kotelyan@plmsc.psu.edu > Pennsylvania State University http://www.plmsc.psu.edu/~kotelyan > University Park, PA 16802, USA ________________________________________________________________________________ > Yes, treating correctly Coulomb interactions in molecular simulations > (without using a cutoff in the list of interacting centers) is indeed an > important topic. The contest seems to have been won by smooth particle > mesh Ewald sums (SPME), which scales as O(N) like the fast multipole > technique, but with a much smaller costant factor, as I am said: see > T.A. Darden, D.M. York, L.G. Pedersen, J. Chem. Phys., 98, 10089 (1993); > U. Essmann, L. Perera, M. Berkowitz, T. Darden, H. Lee, L.G. Pedersen, > J. Chem. Phys., 103, 8577 (1995); P. Procacci and M. Marchi, J. Chem. > Phys., 104, 3003-3012 (1996); P. Procacci, T. Darden, M. Marchi, > J. Phys. Chem., 100, 10464-10468 (1996). > > Two references for the fast multipole method, which I admit to have > never read though, are K.E. Schmidt, M.A. Lee, J.Stat.Phys. 1223-1235 > (1991) and J. Shimada, H. Kaneko, T. Takada, J. Comp. Chem. 15, 28 > (1994). See also the book D.Frenkel, B.Smit, Understanding Molecular > Simulation, Academic Press (1996). > > It's not clear to me, however, if high accuracy and periodic boundary > conditions are needed in docking problems as well as in molecular > dynamics simulations. If they aren't, maybe the fast multipole method > which was originally devised for a cluster of ions is indeed a better > choice than SPME. > > Regards > > Dr. Guido Germano > > Research Assistant in Theoretical Physics, University of Bristol, England > Tel. +44-117-928 8755, http://www.phy.bris.ac.uk/staff/germano_g.html > ________________________________________________________________________________ > There is an abundance of reviews on drug design. Look at the book series, > Reviews in Computational Chemistry, edited by Lipkowitz and myself. > Particularly Vol. 5 (1994) and Vol. 11 (1997). These books will probably be > in your chemistry department library. Also, take a look at the May 1998 issue > of CHEMTECH magazine, p.19. Again it should be in your chemistry department > library. > > Don > Donald B. Boyd, Ph.D. > Editor, Journal of Molecular Graphics and Modelling > Department of Chemistry > Indiana University-Purdue University at Indianapolis > 402 North Blackford Street > Indianapolis, Indiana 46202-3274, U.S.A. > E-mail boyd@chem.iupui.edu ________________________________________________________________________________ > I suggest that you look at papers by S L Price (University College > London) to see applications of multipole calculations in molecular > modelling. However her work may not be directly applicable to > docking calculations: I think she is mainly interested in small- > molecule crystallographic modelling issues. Certainly multipole > calculations are an important technique in that area (although > they are rarely used in practice because the major modelling > software packages cannot handle them at present). I don't know > anything about docking myself so I cannot comment on how useful > they would be in docking calculations. > > -- > John Osborn > University of Bradford, UK. > Email j.c.osborn@bradford.ac.uk -- Don Steiger dons@hamilton.math.missouri.edu From rino@gpc.ibc.wustl.edu Wed Aug 5 13:28:54 1998 Received: from wugate.wustl.edu (wugate.wustl.edu [128.252.120.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA12805 Wed, 5 Aug 1998 13:28:54 -0400 (EDT) Received: from [128.252.137.150] ([128.252.137.150]) by wugate.wustl.edu (8.8.8/8.8.5) with ESMTP id MAA14342; Wed, 5 Aug 1998 12:28:45 -0500 (CDT) Date: Wed, 5 Aug 1998 12:28:45 -0500 (CDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: gamess-users-request@glue.umd.edu From: Rino Ragno Subject: ESTAR Cc: CHEMISTRY@www.ccl.net Hi gamess users and CClers, Is there out there anyone that uses ESTER to calculate the multipoles on large molecules from fragments? Thank to all Ciao -- Rino Ragno ++----------------------------------------------------------------------++ ++----------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: ragno@uniroma1.it || || Institute for Biomedical Computing or: rino@gpc.wustl.edu || || Center for Molecular Design or: ragno@axcasp.caspur.it || || Box8036, Washington University Phone : 314-362-2272 || || 700 South Euclid Avenue FAX : 314-362-0234 || || St. Louis, Missouri 63110 || || U. S. A. || || || || WEB PAGE : www.ibc.wustl.edu/cmd/people/rino/rino.html || || || ++----------------------------------------------------------------------++ ++----------------------------------------------------------------------++ From alkemyst@mailcity.com Wed Aug 5 21:45:59 1998 Received: from mailcity.com (fes.whowhere.com [209.1.236.79]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA15295 Wed, 5 Aug 1998 21:45:58 -0400 (EDT) Received: from Unknown/Local ([?.?.?.?]) by mailcity.com; Wed Aug 5 18:45:27 1998 To: CHEMISTRY@www.ccl.net Date: Wed, 05 Aug 1998 18:45:27 -0700 From: "Alkemyst" Message-ID: Mime-Version: 1.0 X-Sent-Mail: off X-Expiredinmiddle: true X-Mailer: MailCity Service Subject: MOPAC files and CaCHe Visualizer+ X-Sender-Ip: 137.48.14.104 Organization: MailCity (http://www.mailcity.com:80) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am trying to find a way to use UNIX version MOPAC files with a MAC CaCHe Visualizer+. I want to be able to use the speed of the UNIX program and the IR spectra generation capabilities of the CaCHe system. Is there a way to access the UNIX files Visualizer without building and optimizing the molecule on the MAC (I have an older version of CaCHe)? Any help will be appreciated. Thank you for your time. Chris Schwartz Now MailCity offers forwarding so you can check your MailCity messages and other e-mail all in one place. Go to http://www.mailcity.com