Evaluation of enhanced sampling provided by accelerated molecular dynamics with hamiltonian replica exchange methods

Journal of Physical Chemistry B

Volumn 118, Issue 13, 2014, Pages 3543-3552

  Roe, Daniel R ^a   Bergonzo, Christina ^a   Cheatham, Thomas E ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCELERATED MOLECULAR DYNAMICS; ENHANCED SAMPLINGS; FASTER CONVERGENCE; HAMILTONIAN REPLICA EXCHANGE METHODS; MOLECULAR DYNAMICS SIMULATIONS; POTENTIAL BARRIER HEIGHT; RATE OF CONVERGENCE; REPLICA EXCHANGE MOLECULAR DYNAMICS;

HAMILTONIANS; TORSIONAL STRESS;

MOLECULAR DYNAMICS;

RNA;

CHEMISTRY; CLUSTER ANALYSIS; METABOLISM; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS;

CLUSTER ANALYSIS; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; RNA;

EID: 84898068360     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4125099     Document Type: Article

References (52)

1. Shaw, D. E.; Deneroff, M. M.; Dror, R. O.; Kuskin, J. S.; Larson, R. H.; Salmon, J. K.; Young, C.; Batson, B.; Bowers, K. J.; Chao, J. C. Anton, a special-purpose machine for molecular dynamics simulation Commun. ACM 2008, 51 (7) 91-97
2. Götz, A. W.; Williamson, M. J.; Xu, D.; Poole, D.; Le Grand, S.; Walker, R. C. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born J. Chem. Theory Comput. 2012, 8 (5) 1542
3. Salomon-Ferrer, R.; Götz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald J. Chem. Theory Comput. 2013, 9 (9) 3878-3888
4. Henriksen, N. M.; Roe, D. R.; Cheatham, T. E., III. Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations J. Phys. Chem. B 2013, 117 (15) 4014-4027
5. Bergonzo, C.; Henriksen, N. M.; Roe, D. R.; Swails, J. M.; Roitberg, A. E.; Cheatham, T. E. Multi-dimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide J. Chem. Theory Comput. 2014, 10, 492-499
6. Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314 (1) 141-151
7. Wu, X.; Brooks, B. R. Self-guided Langevin dynamics simulation method Chem. Phys. Lett. 2003, 381 (3) 512-518
8. Babin, V.; Roland, C.; Sagui, C. Adaptively biased molecular dynamics for free energy calculations J. Chem. Phys. 2008, 128 (13) 134101-134101
9. Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J. Chem. Phys. 2004, 120, 11919
10. Lednev, I. K.; Karnoup, A. S.; Sparrow, M. C.; Asher, S. A. α-Helix peptide folding and unfolding activation barriers: a nanosecond UV resonance Raman study J. Am. Chem. Soc. 1999, 121 (35) 8074-8086
11. Oliveberg, M.; Tan, Y.-J.; Fersht, A. R. Negative activation enthalpies in the kinetics of protein folding Proc. Natl. Acad. Sci. U.S.A. 1995, 92 (19) 8926-8929
12. Cavalli, A.; Ferrara, P.; Caflisch, A. Weak temperature dependence of the free energy surface and folding pathways of structured peptides Proteins: Struct., Funct., Bioinf. 2002, 47 (3) 305-314
13. Okur, A.; Roe, D. R.; Cui, G.; Hornak, V.; Simmerling, C. Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir J. Chem. Theory Comput. 2007, 3 (2) 557-568
14. Li, H.; Li, G.; Berg, B. A.; Yang, W. Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces J. Chem. Phys. 2006, 125 (14) 144902-144902
15. Lyman, E.; Ytreberg, F. M.; Zuckerman, D. M. Resolution Exchange Simulation Phys. Rev. Lett. 2006, 96 (2) 028105
16. Affentranger, R.; Tavernelli, I.; Di Iorio, E. E. A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling J. Chem. Theory Comput. 2006, 2 (2) 217-228
17. Christen, M.; van Gunsteren, W. F. Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems J. Chem. Phys. 2006, 124 (15) 154106
18. Liu, P.; Voth, G. A. Smart resolution replica exchange: An efficient algorithm for exploring complex energy landscapes J. Chem. Phys. 2007, 126 (4) 045106
19. Fukunishi, H.; Watanabe, O.; Takada, S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction J. Chem. Phys. 2002, 116 (20) 9058-9067
20. Jang, S.; Shin, S.; Pak, Y. Replica-Exchange Method Using the Generalized Effective Potential Phys. Rev. Lett. 2003, 91 (5) 058305
21. Cheng, X.; Cui, G.; Hornak, V.; Simmerling, C. Modified Replica Exchange Simulation Methods for Local Structure Refinement J. Phys. Chem. B 2005, 109 (16) 8220-8230
22. Ostermeir, K.; Zacharias, M. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles J. Comput. Chem. 2014, 35 (2) 150-158
23. de Oliveira, C. A. F.; Hamelberg, D.; McCammon, J. A. Coupling accelerated molecular dynamics methods with thermodynamic integration simulations J. Chem. Theory Comput. 2008, 4 (9) 1516-1525
24. Sinko, W.; de Oliveira, C. A. F.; Pierce, L. C.; McCammon, J. A. Protecting high energy barriers: A new equation to regulate boost energy in accelerated molecular dynamics simulations J. Chem. Theory Comput. 2011, 8 (1) 17-23
25. Yang, L.; Grubb, M. P.; Gao, Y. Q. Application of the accelerated molecular dynamics simulations to the folding of a small protein J. Chem. Phys. 2007, 126, 125102
26. Shen, T.; Hamelberg, D. A statistical analysis of the precision of reweighting-based simulations J. Chem. Phys. 2008, 129 (3) 034103
27. Ceriotti, M.; Brain, G. A.; Riordan, O.; Manolopoulos, D. E. The inefficiency of re-weighted sampling and the curse of system size in high-order path integration Proc. R. Soc. London, Ser. A 2012, 468 (2137) 2-17
28. Markwick, P. R.; McCammon, J. A. Studying functional dynamics in bio-molecules using accelerated molecular dynamics Phys. Chem. Chem. Phys. 2011, 13 (45) 20053-20065
29. Wereszczynski, J.; McCammon, J. A. Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations J. Chem. Theory Comput. 2010, 6 (11) 3285-3292
30. Doshi, U.; Hamelberg, D. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions J. Chem. Theory Comput. 2012, 8 (11) 4004-4012
31. Trebst, S.; Troyer, M.; Hansmann, U. H. Optimized parallel tempering simulations of proteins J. Chem. Phys. 2006, 124, 174903
32. Patriksson, A.; van der Spoel, D. A temperature predictor for parallel tempering simulations Phys. Chem. Chem. Phys. 2008, 10 (15) 2073-2077
33. Mitsutake, A.; Sugita, Y.; Okamoto, Y. Generalized-ensemble algorithms for molecular simulations of biopolymers Pept. Sci. 2001, 60 (2) 96-123
34. Fajer, M.; Hamelberg, D.; McCammon, J. A. Replica-exchange accelerated molecular dynamics (REXAMD) applied to thermodynamic integration J. Chem. Theory Comput. 2008, 4 (10) 1565-1569
35. Jiang, W.; Roux, B. Free energy perturbation hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations J. Chem. Theory Comput. 2010, 6 (9) 2559-2565
36. Arrar, M.; de Oliveira, C. A. F.; Fajer, M.; Sinko, W.; McCammon, J. A. w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations J. Chem. Theory Comput. 2012, 9 (1) 18-23
37. Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional replica-exchange method for free-energy calculations J. Chem. Phys. 2000, 113, 6042-6051
38. Yildirim, I.; Stern, H. A.; Tubbs, J. D.; Kennedy, S. D.; Turner, D. H. Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r (GACC) are improved by revised π torsions J. Phys. Chem. B 2011, 115 (29) 9261-9270
39. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79 (2) 926-935
40. Joung, I. S.; Cheatham, T. E., III. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations J. Phys. Chem. B 2008, 112 (30) 9020-9041
41. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Bioinf. 2006, 65 (3) 712-725
42. Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of alpha/gamma Conformers Biophys. J. 2007, 92 (11) 3817-3829
43. Banáš, P.; Hollas, D.; Zgarbová, M.; Jurečka, P.; Orozco, M.; Cheatham, T. E., III; Šponer, J. i.; Otyepka, M. Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins J. Chem. Theory Comput. 2010, 6 (12) 3836-3849
44. Zgarbová, M.; Otyepka, M.; Šponer, J. i.; Mládek, A. t.; Banáš, P.; Cheatham, T. E., III; Jurecka, P. Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles J. Chem. Theory Comput. 2011, 7 (9) 2886-2902
45. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J. M.; Goetz, A. W.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M. J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. Amber 12; University of California: San Francisco, CA, 2012.
46. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber Biomolecular Simulation Programs J. Comput. Chem. 2005, 26 (16) 1668-1688
47. Darden, T.; York, D.; Pedersen, L. Partical mesh Ewald-an Nlog(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 8577-8593
48. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of cartesian equations of motion of a system with constraints-molecular dynamics of N-alkanes J. Comput. Phys. 1977, 23 (3) 327-341
49. Roe, D. R.; Cheatham, T. E., III. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013, 9, 3084-3095
50. Ester, M.; Kriegel, H. P.; Sander, J.; Xu, X. A density-based algorithm for discovering clusters in large spatial databases with noise. In Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96); Simoudis, E.; Han, J.; Fayyad, U., Eds.; AAAI Press: Palo Alto, CA, 1996; pp 226-231.
51. Kullback, S.; Leibler, R. A. On information and sufficiency Ann. Math. Stat. 1951, 22 (1) 79-86
52. Abraham, M. J.; Gready, J. E. Ensuring mixing efficiency of replica-exchange molecular dynamics simulations J. Chem. Theory Comput. 2008, 4 (7) 1119-1128