Multidimensional replica-exchange method for free-energy calculations
نویسندگان
چکیده
منابع مشابه
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange simulation is performed and the multicanonical weight factor is obtained by the multiple-histogram reweighting techniques. The second one is a further extension of...
متن کاملSatisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange.
An error measure, referred to as the hysteresis error, is developed from the Crooks fluctuation theorem to evaluate the sampling quality in free-energy calculations. Theory and the numerical free energy of hydration calculations are used to show that Hamiltonian replica exchange provides a direct route for minimizing the hysteresis error. Replica exchange swap probabilities yield the rate at wh...
متن کاملGeneralized replica exchange method.
We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of...
متن کاملFrom multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering.
We discuss multidimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential-energy function E0 by adding any physical quantity V of interest as a new energy term with a coupling constant lambda. We then perform a multidimensional multicanonical simulation where a random walk in E0 and V spaces is realized. We ca...
متن کاملw-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD within a Hamiltonian replica exchange fra...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2000
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.1308516