A random walk sampling algorithm allows the extraction of the density of states distribution in energy-reaction coordinate space. As a result, the temperature dependences of thermodynamic quantities such as relative energy, entropy, and heat capacity can be calculated using first-principles statistical mechanics. The strategies for optimal convergence of the algorithm and control of its accuracy are proposed. We show that the saturation of the error [Q. Yan and J. J. de Pablo, Phys. Rev. Lett. 90, 035701 (2003); E. Belardinelli and V. D. Pereyra, J. Chem. Phys. 127, 184105 (2007)] is due to the use of histogram flatness as a criterion of convergence. An application of the algorithm to methane dimer hydrophobic interactions is presented. We obtained a quantitatively accurate energy-entropy decomposition of the methane dimer cavity potential. The presented results confirm the previous results, and they provide new information regarding the thermodynamics of hydrophobic interactions. We show that the finite-difference approximation, which is widely used in molecular dynamic simulations for the energy-entropy decomposition of a free energy potential, can lead to a significant error.
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21 February 2009
Research Article|
February 19 2009
Thermodynamics of a conformational change using a random walk in energy-reaction coordinate space: Application to methane dimer hydrophobic interactions
A. N. Morozov;
A. N. Morozov
a)
1
National Chiao Tung University
, 1001 Ta Hsuen Road, Hsinchu, Taiwan Republic of China
2Institute of Atomic and Molecular Sciences,
Academia Sinica
, P.O. Box 23-166, Taipei, Taiwan 10617, Republic of China
3Institute of Surface Chemistry,
National Academy of Sciences of Ukraine
, Generala Naumova str. 17, Kyiv 03164, Ukraine
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S. H. Lin
S. H. Lin
1
National Chiao Tung University
, 1001 Ta Hsuen Road, Hsinchu, Taiwan Republic of China
2Institute of Atomic and Molecular Sciences,
Academia Sinica
, P.O. Box 23-166, Taipei, Taiwan 10617, Republic of China
Search for other works by this author on:
a)
Electronic mail: [email protected].
J. Chem. Phys. 130, 074903 (2009)
Article history
Received:
October 31 2008
Accepted:
January 12 2009
Citation
A. N. Morozov, S. H. Lin; Thermodynamics of a conformational change using a random walk in energy-reaction coordinate space: Application to methane dimer hydrophobic interactions. J. Chem. Phys. 21 February 2009; 130 (7): 074903. https://doi.org/10.1063/1.3077658
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