GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit

Bioinformatics

Volumn 29, Issue 7, 2013, Pages 845-854

  Pronk, Sander ^a,b   Páll, Szilárd ^a,b   Schulz, Roland ^c,d   Larsson, Per ^e,f   Bjelkmar, Pär ^a,g   Apostolov, Rossen ^a,b   Shirts, Michael R ^h   Smith, Jeremy C ^c,d   Kasson, Peter M ^e,f   Van Der Spoel, David ^a,i   Hess, Berk ^a,b   Lindahl, Erik ^a,b,g  

^a SCIENCE FOR LIFE LABORATORY   (Sweden)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF TENNESSEE   (United States)

^e UNIVERSITY OF VIRGINIA   (United States)

^f University of Virginia   (United States)

^g STOCKHOLM UNIVERSITY   (Sweden)

^h University of Virginia   (United States)

ⁱ UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; MOLECULAR DYNAMICS;

ALGORITHMS; MOLECULAR DYNAMICS SIMULATION; PROTEINS; SOFTWARE;

EID: 84875592758     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt055     Document Type: Article

References (51)

1. Alder, B. and Wainwright, T. (1957) Phase transition for a hard sphere system. J. Chem. Phys., 27, 1208-1209.
2. Bennett, C.H. (1976) Efficient estimation of free energy differences from Monte Carlo data. J. Comp. Phys., 22, 245.
3. Berendsen, H. (1976) Report of CECAM workshop: models for protein dynamics. In: Technical report. CECAM, Lyon.
4. Bowers, K.J. et al. (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the ACM/IEEE Conference on Supercomputing (SC06). ACM, New York, NY.
5. Bowman, G. et al. (2011) Atomistic folding simulations of the five helix bundle protein 6-85. J. Am. Chem. Soc., 133, 664-667.
6. Boyce, S. et al. (2009) Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J. Mol. Biol., 394, 747-763.
7. Brooks, B. et al. (2009) Charmm: The biomolecular simulation program. J. Comp. Chem., 30, 1545-1614.
8. Caleman, C. et al. (2012) Force field benchmark of organic liquids: density, enthalpy of vaporization, heat capacities, surface tension, compressibility, expansion coefficient and dielectric constant. J. Chem. Theor. Comput., 8, 61-74.
9. Case, D. et al. (2005) The amer biomolecular simulation programs. J. Comp. Chem., 26, 1668-1688.
10. Chong, L. et al. (1999) Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48g7. Proc. Natl Acad. Sci. USA, 96, 14330-14335.
11. Christen, M. et al. (2005) The gromos software for biomolecular simulation: Gromos05. J. Comp. Chem., 26, 1719-1951.
12. Duan, Y. and Kollman, P. (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science, 282, 740-744.
13. Essmann, U. et al. (1995) A smooth particle mesh Ewald method. J. Chem. Phys., 103, 8577-8592.
14. Hawkins, D. et al. (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. A, 100, 19824-19839.
15. Helms, V. and Wade, R. (1998) Computational alchemy to calculate absolute protein-ligand binding free energy. J. Am. Chem. Soc., 120, 2710-2713.
16. Hess, B. et al. (2008) Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theor. Comput., 4, 435-447.
17. Huang, D. and Caflisch, A. (2011) The free energy landscape of small molecule unbinding. PLoS Comput. Biol., 7, e1002002.
18. Hub, J.S. et al. (2010) wham-a free weighted histogram analysis implementation including robust error and autocorrelation estimates. J. Chem. Theor. Comput., 6, 3713-3720.
19. Humphrey, W. et al. (1996) VMD - VisualMolecular Dynamics. J. Molec. Graphics, 14, 33-38.
20. Kasson, P.M. et al. (2010) Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. PLoS Comput. Biol., 6, e1000829.
21. Lange, O.F. et al. (2010) Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys. J., 99, 647-655.
22. Larsson, D. et al. (2012) Virus capsid dissolution studied by microsecond molecular dynamics simulations. PLoS Comput. Biol., 8, e1002502.
23. Larsson, P. and Lindahl, E. (2010) A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling. J. Comp. Chem., 31, 2593-2600.
24. Levitt, M. and Lifson, S. (1969) Refinement of protein conformations using a macromolecular energy minimization procedure. J. Mol. Biol., 46, 269-279.
25. Lifson, S. and Warshel, A. (1968) A consistent force field for calculation on conformations, vibrational spectra and enthalpies of cycloalkanes and n-alkane molecules. J. Phys. Chem, 49, 5116-5130.
26. Lindorff-Larsen, K. et al. (2011) How fast-folding proteins fold. Science, 334, 517-520.
27. Malde, A.K. et al. (2011) An automated force field topology builder (ATB) and repository: version 1.0. J. Chem. Theor. Comput., 7, 4026-4037.
28. Marrink, S.J. et al. (2007) The MARTINI force field: Coarse grained model for biomolecular simulations. J. Phys. Chem. B, 111, 7812-7824.
29. Martyna, G.J. et al. (1996) Explicit reversible integrators for extended systems dynamics. Mol. Phys., 87, 1117-1157.
30. McCammon, J. et al. (1977) Dynamics of folded proteins. Nature, 267, 585-590.
31. Murail, S. et al. (2011) Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor. Biophys J., 100, 1642-1650.
32. Noé, F. and Fischer, S. (2008) Transition networks for modeling the kinetics of conformational change in macromolecules. Curr. Opin. Struct. Biol., 18, 154-162.
33. Nosé, S. and Klein, M.L. (1983) Constant pressure molecular dynamics for molecular systems. Mol. Phys., 50, 1055-1076.
34. Nury, H. et al. (2010) One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl Acad. Sci. USA, 107, 6275-6280.
35. Onufriev, A. et al. (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins, 55, 383-394.
36. Pande, V. et al. (2010) Everything you wanted to know about Markov state models but were afraid to ask. Methods, 52, 99-105.
37. Parrinello, M. and Rahman, A. (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys., 52, 7182-7190.
38. Phillips, J. et al. (2005) Scalable molecular dynamics with namd. J. Comp. Chem., 26, 1781-1802.
39. Qui, D. et al. (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii. J. Phys. Chem. A, 101, 3005-3014.
40. Schulz, R. et al. (2009) Scaling of multimillion-atom biological molecular dynamics simulation on a petascale supercomputer. J. Chem. Theor. Comput., 5, 2798-2808.
41. Shirts, M.R. and Pande, V.S. (2005) Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J. Chem. Phys., 122, 144107.
42. Swope, W.C. et al. (1982) A computer-simulation method for the calculation of equilibrium-constants for the formation of physical clusters of molecules: application to small water clusters. J. Chem. Phys., 76, 637-649.
43. Valiev, M. et al. (2010) NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comput. Phys. Commun., 181, 1477-1489.
44. van der Spoel, D. and Hess, B. (2011) Gromacs - the road ahead. WIREs Comput. Mol. Sci., 1, 710-715.
45. van der Spoel, D. and Seibert, M. (2006) Protein folding kinetics and thermodynamics from atomistic simulations. Phys. Rev. Lett., 96, 238102-238106.
46. van der Spoel, D. and van Maaren, P.J. (2006) The origin of layer structure artifacts in simulations of liquid water. J. Chem. Theor. Comput., 2, 1-11.
47. van der Spoel, D. et al. (2012) GROMACS molecule and liquid database. Bioinformatics, 28, 752-753.
48. Vanommeslaeghe, K. et al. (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem., 31, 671-690.
49. Wang, J. et al. (2005) Antechamber, an accessory software package for molecular mechanical calculations. J. Comput. Chem., 25, 1157-1174.
50. Wold, M. et al. (2010) membed: efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J. Comp. Chem., 31, 2169-2174.
51. Zhang, J. et al. (2011) Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure, 19, 1784-1795.