Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal

Proteins: Structure, Function and Genetics

Volumn 43, Issue 4, 2001, Pages 509-519

  Walser, Regula ^a   Hünenberger, Philippe H ^a   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Counter ions; Electrostatic interactions; Molecular dynamics simulations; Particle particle particle mesh method; Reaction field correction

Indexed keywords

UBIQUITIN;

ANALYTIC METHOD; ARTICLE; CRYSTAL; CRYSTAL STRUCTURE; ELECTROCHEMISTRY; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN INTERACTION; REACTION ANALYSIS; REPRODUCIBILITY; SIMULATION; STRUCTURE ANALYSIS; VALIDATION PROCESS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; CRYSTALLIZATION; DIFFUSION; ELECTROSTATICS; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTONS; THERMODYNAMICS; TIME FACTORS; UBIQUITINS;

EID: 17144471008     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1062     Document Type: Article

References (26)

1. van Gunsteren WF, Berendsen HJC. GROningen MOlecular Simulation (GROMOS) library manual. Nijenborgh 4, 9747 AG Groningen, The Netherlands: Biomos; 1987.
2. van Gunsteren WF, Berendsen HJC. Computer simulation of molecular dynamics: methodology, applications and perspectives in chemistry. Angew Chem Int Ed Engl 1990;29:992-1023.
3. Schreiber H, Steinhauser O. Molecular dynamics studies of solvated polypeptides: why the cut-off scheme does not work. Chem Phys 1992;168:75-89.
4. Tironi IG, Sperb R, Smith PE, van Gunsteren WF. A generalized reaction-field method for molecular dynamics simulations. J Chem Phys 1995;102:6199-6207.
5. Auffinger P, Beveridge DL. A simple test for evaluating the truncation effects in simulations of systems involving charged groups. Chem Phys Letters 1995;234:413-415.
6. Cheatham III TE, Miller JL, Fox T, Darden TA, Kollman PA. Molecular dynamics simulation on solvated biomolecular systems: the particle-mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 1995;117:4193-4194.
7. Fox T, Kollman PA. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"? Proteins 1996;25:315-334.
8. Stocker U. Computer simulation of biomolecules: investigation of molecular environment and simulation parameters. Ph.D. thesis, ETH Zürich, Switzerland, 2000.
9. Ewald PP. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann Phys 1921;64:253-287.
10. Allen MP, Tildesley DJ. Computer simulation of liquids. Oxford, UK: Clarendon; 1987.
11. Hockney RW, Eastwood JW. Computer simulations using particles. New York: McGraw-Hill; 1981.
12. Weber W, Hünenberger PH, McCammon JA. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J Phys Chem B 2000;104:3668-3675.
13. Ibragimova GT, Wade RC. Importance of explicit salt ions for protein stability in molecular dynamics simulation. Biophys J 1998;74:2906-2911.
14. van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG. Biomolecular simulation: the GROMOS96 manual and user guide. ETH Zürich, Switzerland: vdf Hochschulverlag; 1996.
15. Scott WRP, Hünenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda A, Huber T, Krüger P, van Gunsteren WF. The GROMOS biomolecular simulation program package. J Phys Chem 1999;103:3596-3607.
16. Vijay-Kumar S, Bugg CE, Cool WJ. Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 1987;194:531-544.
17. Bernstein FC, Koetzle TF, Williams GJB, Meyer Jr. EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macro-molecular structures. J Mol Biol 1977;112:535-542.
18. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht: Reidel; 1981. p 331-342.
19. Stocker U, van Gunsteren WF. Molecular dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin. Intl Tables for Crystallography 2000; F. In press.
20. Smith PE, van Gunsteren WF. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K. J Chem Phys 1994;100:3169-3174.
21. Hünenberger PH. Lattice-sum methods for computing electrostatic interactions in molecular simulations. In: Hummer G, Pratt LR, editors. Simulation and theory of electrostatic interactions in solution: computational chemistry, biophysics, and aqueous solution. New York: American Institute of Physics; 1999. p 17-83.
22. Deserno M, Holm C. How to mesh up Ewald sums. II. An accurate error estimate for the particle-particle-particle-mesh algorithm. J Chem Phys 1998;109:7694-7701.
23. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
24. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Chem 1977;23:327-341.
25. Frishman D, Argos P. Knowledge-based secondary structure assignment. Proteins 1995;23:566-579.
26. Becke M, editor. Gmelin Handbuch der anorganischen Chemie. 8th edition. Berlin: Springer Verlag; 1974.