From bruno@antas.agraria.uniss.it Sun May 3 16:28:38 1998 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id PAA05169; Sun, 3 May 1998 15:48:14 -0400 (EDT) Received: from pippo.uniss.it (dial2.uniss.it [193.204.207.92]) by ssmain.uniss.it with SMTP (8.8.8/8.8.8) id VAA29515 for ; Sun, 3 May 1998 21:48:21 +0200 (METDST) Message-ID: <354B6A7A.7215@antas.agraria.uniss.it> Date: Sat, 02 May 1998 20:48:27 +0200 From: bruno Organization: University of Sassari X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Summary: Convergent Lattice Sum for Lennard-Jones terms Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A few days ago I mailed the following message: >I've heard about the use of convergent lattice sum for Lennard Jones >terms in MD computations. This should have been done by Willians some >decade ago. As far as I know, I don't remember MD simulations involving >the use of such technique, as well as I do not know of any largely used >MD software which implements it. Probably this is due to the peculiar >short range nature of the LJ interactions which make this correction >less important than the use of ewald sums for coulombic forces. Am I >wrong? >Do anyone has some considerations at this regard or can suggest some >readings on this subject? I thank all people who answered and report here a summary of their mails: ------------------------------------------------------------------------ Darden and co-workers have published on using the particle mesh Ewald technique to perform the 1/r**6 part of the LJ terms in Essman et al., J. Chem. Phys. 103, 8577 (1995), "A smooth particle mesh Ewald method". While this method works well for potentials applying geometric combining rules (such as GROMOS) and only involves a single reciprocal space calculation, with Lorentz-Bertholet combining rules (rij = (ri + rj)/2, such as in CHARMM or AMBER) this requires 7 reciprocal space calculations and is therefore prohibitively expensive. Moreover, as you mention, the correction is likely small, although it may be necessary in crystal simulation. Good luck with your search, Thomas Cheatham, III CBS, NHLBI, 12A/2041 National Institute of Health Bethesda, MD 20892-5626 cheatham@helix.nih.gov (301) 402-0617 FAX: (301) 496-2172 ------------------------------------------------------------------------ From: Andrew Rohl The MSI product discover has had the ability to do this as long as I have used it! If you want something a little less expensive, I can recommend GULP from julian gale at Imperial College, London which is I believe free to academic institutions Andrew ------------------------------------------------------------------------ I suggest you look at the book of Hockney and Easwtwood: @Book{Hockney81, author = "R. W. Hockney and J. W. Eastwood", title = "Computer simulation using particles", publisher = "McGraw-Hill", year = "1981", address = "New York", We are currently busy implementing the dispersion term in the GROMACS package: http://rugmd0.chem.rug.nl/~gmx Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------------------------------------------------ bruno manunza writes: > I've heard about the use of convergent lattice sum for Lennard Jones > terms in MD computations. This should have been done by Willians some > decade ago. D. E. Williams, Acta Cryst A27 (1971) 4680-4684. There's also a discussion in M.T. Dove, "Introduction to Lattice Dynamics" (1993) Cambridge University Press in Appendix A. > As far as I know, I don't remember MD simulations involving > the use of such technique, as well as I do not know of any largely used > MD software which implements it. I have a vague recollection that Martin Dove might have done this, but in general it isn't worth the effort. You really need it for r**(-1) and r**(-3) porentials where the sum is long-ranged and conditionally convergent, but in the case of a r**(-6) potential there is rapid convergence in real space. Keith Refson ------------------------------------------------------------------------ Within Cerius2 Open Force Field ( used in Cerius2 MD, mechanics, ... ) the vdW r^{-6} is treated by an Ewald summation, based on: @article{ Author = "Karaswa N. and Goddard III W.A.", Title ="", Journal = "J. Phys. Chem.", Volume = 93, Pages = "7320--", Year = 1989} Simon Dr Simon Miller (simonm@msi.com) : Web : http://www.msi.com Molecular Simulations. : ------------------------------------------------------------------------ From: Konrad Hinsen > MD software which implements it. Probably this is due to the peculiar > short range nature of the LJ interactions which make this correction > less important than the use of ewald sums for coulombic forces. Am I > wrong? Right. Electrostatic sums are conditionally convergent, which presents some major problems. LJ sums are well-behaved, and sufficiently short-ranged that a finite cutoff can usually be compensated with a correction term (see the book by Allen & Tildesley for this). Nevertheless, LJ terms can be treated better, either by explicit summation, or by techniques known from electrostatics, i.e. Ewald-like formulas or fast multipole techniques. The only problem with the latter techniques is that they require purely multiplicative combination rules for the LJ parameters of different atom species, whereas many force fields are designed with a combination rule that uses the average of the vdW-radii. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- ------------------------------------------------------------------------ There is a summary of this technique in the International Tables for Crystallography, Volume B, p. 374. -Donald Williams -- Dr. Donald E. Williams email:dew01@xray5.chem.louisville.edu Department of Chemistry University of Louisville phone:502-852-5975 Louisville, KY 40292 fax: 502-852-8149 ----------------------------------------------------------------------- Dear Dr. Manunza, In response to your recent query on the CCL about use of convergent lattice sum expressions for the Lennard Jones potential, we have recently been working with convergent lattice sum expressions for the Lennard Jones potential. Our initial interest was in developing an extended potential accurately calculated for solid phase problems, but then realized that it also has application for MC and MD. We generalized the forms derived by Van Der Hoff and Benson to the triclinic case for our solids applications. For MC or MD use, that is unnecessary. We developed some functional code for MC calculations and have compared its performance with the conventional algorithm with a cutoff radius. For conventional fluid simulations, the convergent sum expressions in our hands yield longer compute times than the conventional algorithm. For problems involving solid phases, the use of the convergent sum algorithm should mean that the simulation can obtain suitable reliability with many fewer atoms in the simulation. This gives a distinct computational advantage. We are pursuing this point. I would appreciate hearing of any work you pursue or of others in this area. Bill Fink, Professor of Chemistry, University of California, Davis,CA, USA whfink@ucdavis.edu ---------------------------------------------------------------------- -- Dr Bruno Manunza DISAABA - Environmental Sciences Dept. V.le ITALIA 39 07100 SASSARI, ITALY phone 39 79 229215 fax 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it http://antas.agraria.uniss.it