A Guide to Monte Carlo for Statistical Mechanics: 2. Byways

Valleau, J. P.; Torrie, G. M.

doi:10.1007/978-1-4684-2553-6_5

Cited by 140 publications

(118 citation statements)

References 74 publications

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“…4 Specifically, we have developed an integrated path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method for computing KIEs, in which molecular dynamics simulations are first carried out to obtain the classical mechanical PMF using umbrella sampling. 47,48 Then, the nuclear coordinates of atoms associated with the chemical reaction are quantized by a path integral with the constraint that the centroid positions coincide with their corresponding classical coordinates. KIEs are evaluated by FEP between heavy and light atom masses, which is related to the quantized quasiparticle positions.…”

Section: Integrated Centroid Path Integral-free Energy Perturbation Amentioning

confidence: 99%

“…46 The PMF profile is obtained using the umbrella sampling technique. 47 In this approach, the reaction is divided into a series of segments called simulation "windows," in which a biasing potential is applied to allow sufficient sampling of high-energy regions along the reaction pathway. The effect of the biasing potential is subsequently removed when the separate simulation windows are combined to produce the overall PMF by using the weighted histogram analysis method.…”

Section: Simulation Detailsmentioning

confidence: 99%

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Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

2007

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An integrated Feynman path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI-FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain-Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain-Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution.

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Section: Integrated Centroid Path Integral-free Energy Perturbation Amentioning

confidence: 99%

Section: Simulation Detailsmentioning

confidence: 99%

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

2007

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“…It has been common practice to carry out standard MC simulations (reviewed by Valleau & Torrie, 1977;Valleau & Whittington, 1977) by performing 2 consecutive sets of simulations. In the first short set, optimized values of the relevant parameters are obtained.…”

Section: The Monte Carlo Methodsmentioning

confidence: 99%

Monte Carlo study of the effect of β₂‐microglobulin on the binding cleft of the HLA‐A2 complex

et al. 1994

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Peptide recognition by class I products of the major histocompatibility complex requires association of the class I heavy chain with /32-microglobulin. We present results of Monte Carlo simulations of the @-pleated sheet floor of the human class I MHC molecule, HLA-A2, with and without P,-microglobulin. We find a significant effect of µglobulin on the side chains of residues near a region that would accommodate the C-terminus of a bound peptide. By modeling simultaneously each loop and its neighboring strand at either end of the class I cleft, we find that P2-microglobulin restricts the conformational space of residues that are central to binding peptides. The effect is most pronounced for R97 and H114 and somewhat less important for Y99 and Y116, the latter forming strong hydrogen bonds with neighboring residues in the heavy chain itself.

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“…Here only the potential energy function ! U(r 1 ,r 2 ,...,r N ) is required to calculate the probability of accepting random particle displacement moves (and additional moves depending on the ensemble type 61,123 ). All of the discussion above regarding the boundary conditions, treatment of long-range interactions and ensembles applies as well to MC simulations.…”

Section: Comments About Monte Carlo Simulationsmentioning

confidence: 99%

Reactivity and Dynamics at Liquid Interfaces

Benjamin¹

2015

Reviews in Computational Chemistry

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A Guide to Monte Carlo for Statistical Mechanics: 2. Byways

Cited by 140 publications

References 74 publications

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

Monte Carlo study of the effect of β₂‐microglobulin on the binding cleft of the HLA‐A2 complex

Reactivity and Dynamics at Liquid Interfaces

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A Guide to Monte Carlo for Statistical Mechanics: 2. Byways

Cited by 140 publications

References 74 publications

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

Monte Carlo study of the effect of β2‐microglobulin on the binding cleft of the HLA‐A2 complex

Reactivity and Dynamics at Liquid Interfaces

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Monte Carlo study of the effect of β₂‐microglobulin on the binding cleft of the HLA‐A2 complex