Evaluation of a grid based molecular dynamics approach for polypeptide simulations

IEEE Transactions on Nanobioscience

Volumn 6, Issue 3, 2007, Pages 229-234

  Merelli, Ivan ^a   Morra, Giulia ^a   Milanesi, Luciano ^a  

^a Institute for Biomedical Technology   (Italy)

Author keywords

Distributed approach; Grid platform; Molecular dynamics

Indexed keywords

COMPUTER SIMULATION; DATA TRANSFER; GRID COMPUTING; MACROMOLECULES; POLYPEPTIDES; PROBLEM SOLVING;

BIOLOGICAL MACROMOLECULES; BIOMEDICAL RESEARCH; DISTRIBUTED APPROACH; KWD GRID PLATFORMS; NEWTON'S EQUATIONS;

MOLECULAR DYNAMICS;

POLYPEPTIDE; PEPTIDE;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; SIMULATION; ALGORITHM; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; KINETICS; PROTEIN CONFORMATION;

ALGORITHMS; COMPUTER SIMULATION; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION;

EID: 36048989903     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2007.903483     Document Type: Article

References (19)

1. M. Taufer, E. Perathoner, A. Cavalli, A. Caflish, and T. Stricker, "Performance characterization of a molecular dynamics code on PC clusters - Is there any easy parallelism in CHARMM," in Proc. IPDPS, 2002.
2. J. Hein, F. Reid, L. Smith, I. Bush, M. Guest, and P. Sherwood, "On the performance of molecular dynamics applications on current high-end systems," Phil. Trans. Math. Phys. Eng. Sci. 2005, vol. 363, 1987-1998.
3. J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. Skeel, L. Kale, and K. Schulten, "Scalable molecular dynamics with NAMD.," J. Comp. Chem., vol. 26, pp. 1781-1802, 2005.
4. A. R. Fersht, "On the simulation of protein folding by short time scale molecular dynamics and distributed computing," Proc. Nat. Acad. Sci. USA, vol. 99, pp. 14 122-14 125, 2002.
5. M. R. Shirts and V. S. Pande, "Mathematical analysis of coupled parallel simulations," Phys. Rev. Lett., vol. 86, pp. 4983-4987, 2001.
6. B. Zagrovic, E. J. Sorin, and V. S. Pande, "Beta-hairpin folding simulations in atomistic detail using an implicit solvent model," J. Mol. Biol., vol. 313, pp. 151-169, 2001.
7. V. S. Pande, I. Baker, J. Chapman, S. Elmer, S. Khaliq, S. Larson, M. Y. Rhee, M. R. Shirts, C. Snow, E. J. Sorin, and B. Zagrovic, "Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing," Biopolymers, vol. 68, pp. 91-109, 2003.
8. C. D. Snow, H. Nguyen, V. S. Pande, and M. Gruebele, "Absolute comparison of simulated and experimental protein-folding dynamics," Nature, vol. 420, pp. 33-34, 2002.
9. D. K. Klimov, D. Newfield, and D. Thirumalai, "Simulations of beta-hairpin folding confined to spherical pores using distributed computing," Proc. Natl. Acad. Sci. USA, vol. 99, pp. 8019-8024, 2002.
10. A. Natrajan, M. Crowley, N. Wilkins-Diehr, M. A. Humphrey, A. D. Fox, A. S. Grimshaw, and C. L. Brooks, "Studying protein folding on the grid: Experiences using CHARMM on NPACI resources using Legion," Concurrency Computat. Pract. Exper., vol. 16, pp. 285-397, 2004.
11. C. J. Woods, M. H. Ng, S. Johnston, S. E. Murdock, B. Wu, H. Fanghor, P. Jeffreys, S. Cox, J. G. Frey, M. S. Sansom, and J. W. Essex, "Grid computing and biomolecular simulation," Philos. Trans. Math. Phys. Eng. Sci., vol. 15, no. 20, pp. 17-35, 2005.
12. E. Paci, A. Cavalli, M. Vendruscolo, and A. Caflisch, "Analysis of the distributed computing approach applied to the folding of a small beta peptide," Proc. Natl. Acad. Sci. USA, vol. 100, pp. 8217-8222, 2003.
13. M. Gower, J. Cohen, J. Phillips, R. Kufrin, and K. Schulten, "Managing biomolecular simulations in a grid environment with NAMD-G.," in Proc. 2006 TeraGrid Conf..
14. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, "CHARMM: A program for macromolecular energy, minimization and dynamics calculations," J. Comp. Chem., vol. 4, pp. 187-217, 1983.
15. I. Foster and C. Kesselman, "Globus: A metacomputing infrastructure toolkit," Int. J. Supercomput. Appl., vol. 11, no. 2, pp. 115-128, 1997.
16. R. Alfieri, R. Barbera, A. Cavalli, R. Cecchini, A. Chierici, V. Ciaschini, L. Dell'Angelo, F. Donno, E. Ferro, A. Fortem, L. Gaido, A. Gianoli, A. Ghiselli, A. Italiano, S. Lusso, P. Mastroserio, D. Mura, M. Serra, M. Reale, L. Salconi, F. Spataro, F. Taurino, G. Tortone, D. Vicinanza, and G. V. Finzi, The INFN - GRID testbed INFN Tech. Rep., Nov. 2002.
17. H. D. Arndt, D. Bockelmann, A. Knoll, S. Lamberth, C. Griesinger, and U. Koert, "Kationenkontrolle bei der funktionsprogrammierung von helices: Strukturenines D,L-Peptid-Ionenkanals," Angew. Chem., vol. 114, pp. 4234-4238, 2002.
18. G. Morra, U. Koert, and E. W. Knapp, "Role of ions on structure and stability of a synthetic gramicidin ion channel in solution. A molecular dynamics study. J. Phys.," Chem. B, vol. 109, pp. 10 441-10 448, 2005.
19. D. A. Pearlman, D. A. Case, J. W. Caldwell, W. R. Ross, T. E. Cheatharm, S. De Bolt, D. Ferguson, G. Seibel, and P. Kollman, "AMBER a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules.," Comp. Phys. Commun., vol. 91, pp. 1-41, 1995.