On the convergence of multi-scale free energy simulations
نویسندگان
چکیده
منابع مشابه
Escorted free energy simulations: improving convergence by reducing dissipation.
Nonequilibrium, "fast switching" estimates of equilibrium free energy differences DeltaF are often plagued by poor convergence due to dissipation. We propose a method to improve these estimates by generating trajectories with reduced dissipation. Introducing an artificial flow field that couples the system coordinates to the external parameter driving the simulation, we derive an identity for D...
متن کاملConvergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations.
Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined quantum mechanics and molecular mechanics (QM/MM) level, e.g. for enzyme reactions. Such calculations require extensive sampling of phase space, which typically is prohibitive with density-functional theory or ab initio methods. Therefore, such calculations have mostly been performed with semiempi...
متن کاملEscorted free energy simulations.
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 [C. Jarzynski, Phys. Rev. E 65, 046122 (2002)] to nonequilibrium switching simulations, and involves generating artificial, "escorted" trajectories by coupling the evolution of the sy...
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A novel method for the calculation of the free energy difference between two states of a molecular system is presented. The method, an extension of thermodynamic integration, treats the coupling parameter k as a variable in an extended Hamiltonian formulation and propagates it with the physical coordinates. In the resulting generalized ensemble, the crossing of barriers in the physical space is...
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قاعده مقتضی و مانع در متون فقهی کم و بیش مستند احکام قرار گرفته و مورد مناقشه فقهاء و اصولیین می باشد و مشهور معتقند مقتضی و مانع، قاعده نیست بلکه یکی از مسائل ذیل استصحاب است لذا نگارنده بر آن شد تا پیرامون این قاعده پژوهش جامعی انجام دهد. به عقیده ما مقتضی دارای حیثیت مستقلی است و هر گاه می گوییم مقتضی احراز شد یعنی با ماهیت مستقل خودش محرز گشته و قطعا اقتضاء خود را خواهد داشت مانند نکاح که ...
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ژورنال
عنوان ژورنال: Molecular Simulation
سال: 2018
ISSN: 0892-7022,1029-0435
DOI: 10.1080/08927022.2018.1475741