Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes

Radmer, Randall J.; Kollman, Peter A.

doi:10.1002/(sici)1096-987x(199705)18:7<902::aid-jcc4>3.0.co;2-v

Cited by 102 publications

(82 citation statements)

References 28 publications

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“…This suggest that the GEMC technique can yield Gibbs free energies of transfer with relative statistical error smaller than 2%. This level of statistical error appears to be a major improvement compared to the errors encountered in more traditional free energy calculations [24].…”

Section: Resultsmentioning

confidence: 90%

Calculating Gibbs free energies of transfer from Gibbs ensemble Monte Carlo simulations

Martin

Siepmann

1998

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

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The partitioning of the ternary systems npentane/n-heptane/(helium or argon) at ambient conditions is investigated using con®gurational-bias Monte Carlo simulations in the Gibbs ensemble. The results demonstrate that this approach yields very precise partition constants and free energies of transfer. Simulations are carried out to study the dependence of the npentane partitioning with respect to the carrier gas, the system size, and the overall solute concentrations. None of the changes of variables, within the ranges used here, has a signi®cant eect on the alkane partitioning. However, chemical potentials calculated via Widom's ghost particle insertions show a strong number dependence for phases containing relatively few molecules of a given type. This problem originates from the fact that the chemical potential is calculated for a concentration of real particles plus one ghost particle that is systematically larger than the equilibrium concentration. A simple correction term is suggested to account for this problem.

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Section: Resultsmentioning

confidence: 90%

Calculating Gibbs free energies of transfer from Gibbs ensemble Monte Carlo simulations

Martin

Siepmann

1998

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

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“…The Bennett estimator, Eq. 38 can be rewritten as a ratio of two free energy perturbation identities [39] P H (W )/P F (W ) P F (W ) P H (W )/P R (−W ) P R (−W ) = 1 (A1)…”

Section: B Dipole Fluidmentioning

confidence: 99%

Escorted free energy simulations

Vaikuntanathan¹,

Jarzynski²

2011

The Journal of Chemical Physics

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We describe a strategy to improve the efficiency of free energy estimates by reducing dissipation in nonequilibrium Monte Carlo simulations. This strategy generalizes the targeted free energy perturbation approach [Phys. Rev. E. 65, 046122, 2002] to nonequilibrium switching simulations, and involves generating artificial, "escorted" trajectories by coupling the evolution of the system to updates in external work parameter. Our central results are:(1) a generalized fluctuation theorem for the escorted trajectories, and (2) estimators for the free energy difference ∆F in terms of these trajectories. We illustrate the method and its effectiveness on model systems.

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“…We scaled the full CO 2 -H 2 O interactions linearly: ε CO 2 (λ) = λ · ε full CO 2 and q CO 2 (λ) = λ · q full CO 2 . We chose the λ's in such a way to ensure that a change in the absolute value of µ ex,∞ i (T, V ) between two neighboring λ's was less than 2k B T [36]. Typically, 12 independent NPT MC simulation runs were needed at T = 275 K and five simulations were sufficient at T = 500 K. The independent NPT MC simulation runs were efficiently distributed and carried out on SHARCNET using the MPI library.…”

Section: Simulation Detailsmentioning

confidence: 99%

Analysis of Henry’s constant for carbon dioxide in water via Monte Carlo simulation

Lı́sal¹,

Smith²,

Aim³

2005

Fluid Phase Equilibria

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We present calculations of the Henry constant for carbon dioxide in water by Monte Carlo simulations over a broad range of temperatures, from 0 • C to the critical temperature of water. A range of intermolecular potential models is examined for each species. Carbon dioxide is modelled by two three-site (EPM2, and Errington and Panagiotopoulos) potentials and water is modelled by four three-site (SPC, SPC/E, MSPC/E, and Errington and Panagiotopoulos) potentials, by the four-site TIP4P potential and by the five-site TIP5P potential. Henry's constant is computed via the Widom test-particle insertion method and by means of a staged free-energy perturbation method. The performance of the various potential models with respect to the accuracy of their prediction of the Henry constant is discussed. The staged free-energy perturbation method, employed at several representative temperatures, allows further analysis of the Henry constant with respect to the free energy of cavity formation for hosting the CO 2 solute molecule in the H 2 O solvent and the free energy of interactions between the CO 2 solute molecule and the H 2 O solvent. We found that all CO 2 /H 2 O models predicted a qualitatively correct temperature dependence of the Henry constant but only the Errington and Panagiotopoulos CO 2 /H 2 O model gave values for the Henry constant in reasonable agreement with experimental data.

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Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes

Cited by 102 publications

References 28 publications

Calculating Gibbs free energies of transfer from Gibbs ensemble Monte Carlo simulations

Calculating Gibbs free energies of transfer from Gibbs ensemble Monte Carlo simulations

Escorted free energy simulations

Analysis of Henry’s constant for carbon dioxide in water via Monte Carlo simulation

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