Effect of the integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration

Journal of Chemical Theory and Computation

Volumn 6, Issue 4, 2010, Pages 1018-1027

  Jorge, Miguel ^a   Garrido, Nuno M ^a   Queimada, António J ^a   Economou, Ioannis G ^b,c   MacEdo, Eugénia A ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY   (Greece)

^c KHALIFA UNIVERSITY   (United Arab Emirates)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77951141262     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct900661c     Document Type: Article

References (38)

1. Gilson, M.; Zhou, H. Calculation of protein-ligand binding affinities Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21-42
2. Jorgensen, W. L. The many roles of computation in drug discovery Science 2004, 303 (5665) 1813-1818
3. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations J. Chem. Theory Comput. 2009, 5 (2) 350-358
4. Guthrie, J. P. A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview J. Phys. Chem. B 2009, 113 (14) 4501-4507
5. Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 2004, 25 (13) 1656-1676
6. Kirkwood, J. G. Statistical Mechanics of Pure Fluids J. Chem. Phys. 1935, 3, 300-313
7. Chipot, C.; Pohorille, A. Free Energy Calculations-Theory and Applications in Chemistry and Biology; Springer: Berlin, 2007.
8. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins J. Chem. Phys. 2003, 119 (11) 5740-5761
9. Straatsma, T.; Berendsen, H. Free energy of ionic hydration: analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations J. Chem. Phys. 1988, 89, 5876-5886
10. + in the ice/water interface J. Chem. Phys. 2005, 123 034706
11. Swope, W.; Andersen, H. A molecular dynamics method for calculating the solubility of gases in liquids and the hydrophobic hydration of inert-gas atoms in aqueous solution J. Phys. Chem. 1984, 88, 6548-6556
12. Hummer, G.; Pratt, L. R.; Garca, A. E. Free energy of ionic hydration J. Phys. Chem. 1996, 100 (4) 1206-1215 (Pubitemid 126835015)
13. Shyu, C.; Ytreberg, F. M. Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic data J. Comput. Chem. 2009, 30, 2297-2304
14. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
15. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118 (45) 11225-11236 (Pubitemid 26399746)
16. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The missing term in effective pair potentials J. Phys. Chem. 1987, 91 (24) 6269-6271
17. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18 (12) 1463-1472 (Pubitemid 127637344)
18. Miyamoto, S.; Kollman, P. A. SETTLE-An Analytical Version of the SHAKE and RATTLE agorithm for Rigid Water Molecules J. Comput. Chem. 1992, 13 (8) 952-962
19. Garrido, N. M.; Jorge, M.; Queimada, A. J.; Economou, I. G.; Macedo, E. A. Molecular Simulation of the Hydration Gibbs Energy of Barbiturates. Fluid Phase Equilib. 2010, 289, 148-155
20. Lee, F. S.; Warshel, A. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations J. Chem. Phys. 1992, 97 (5) 3100-3107
21. van Gunsteren, W.; Berendsen, H. A leap-frog algorithm for stochastic dynamics Mol. Simul. 1988, 1 (3) 173-185
22. Van Gunsteren, W. F.; Berendsen, H. J. C. Algorithms for Brownian Dynamics Mol. Phys. 1982, 45 (3) 637-647
23. Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81 (8) 3684-3690
24. Beuler, T. M. R.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations Chem. Phys. Lett. 1994, 222, 529-539
25. Pitera, J. W.; Van Gunsteren, W. F. A comparison of non-bonded scaling approaches for free energy calculations Mol. Simul. 2002, 28 (1-2) 45-65
26. Mobley, D. L.; Dumont, E.; Chodera, J. D.; Dill, K. A. Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent J. Phys. Chem. B 2007, 111 (9) 2242-2254 (Pubitemid 46447557)
27. Liu, D. C.; Nocedal, J. On the Limited Memory BFGS Method for Large Scale Optimization Math. Program. 1989, 45 (3) 503-528 (Pubitemid 20660315)
28. Flyvbjerg, H.; Petersen, H. Error estimates on averages of correlated data J. Chem. Phys. 1989, 91 (1) 461-466
29. Press, W.; Teukolsky, S.; Vetterling, W.; Flannery, B. Numerical recipes in C, 2nd ed.; Cambridge University Press: Cambridge, U. K., 1992.
30. Pierotti, R. A. A scaled particle theory of aqueous and nonaqueous solution Chem. Rev. 1976, 76 (6) 717-726
31. Stillinger, F. H. Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory J. Sol. Chem. 1973, 2 (2/3) 141-158
32. Reiss, H.; Frisch, H. L. Statistical mechanics of rigid spheres J. Chem. Phys. 1959, 31 (2) 369-380
33. Westergren, J.; Lindfors, L.; Hoglund, T.; Luder, K.; Nordholm, S.; Kjellander, R. In silico prediction of drug solubility: 1. Free energy of hydration J. Phys. Chem. B 2007, 111 (7) 1872-1882 (Pubitemid 46384280)
34. Grace Software is available free of charge at http://plasma-gate. weizmann.ac.il/Grace/ (acessed October 22, 2009).
35. Wan, S. Z.; Stote, R. H.; Karplus, M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes J. Chem. Phys. 2004, 121 (19) 9539-9548 (Pubitemid 40001718)
36. Garrido, N. M.; Queimada, A. J.; Jorge, M.; Economou, I. G.; Macedo, E. A. Molecular Simulation of Absolute Hydration Gibbs Energies of Polar Compounds. Submitted for Publication, 2010.
37. Michielan, L.; Bacilieri, M.; Kaseda, C.; Moro, S. Prediction of the Aqueous Solvation Free Energy of Organic Compounds by Using Autocorrelation of Molecular Electrostatic Potential Surface Properties Combined with Response Surface Analysis Bioorg. Med. Chem. 2008, 16 (10) 5733-5742 (Pubitemid 351694465)
38. Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. Group Contributions to the Thermodynamic Properties of Non-Ionic Organic Solutes in Dilute Aqueous Solution J. Sol. Chem. 1981, 10 (8) 563-595