Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations.
作者： Yilin Meng , Danial Sabri Dashti , Adrian E. Roitberg
DOI: 10.1021/CT200153U
关键词: Replica 、 Free energies 、 Conformational sampling 、 Molecular dynamics 、 Hamiltonian (quantum mechanics) 、 Theoretical computer science 、 Free energy perturbation 、 Statistical physics 、 Thermodynamic integration 、 Physics
摘要: Alchemical free energy calculations play a very important role in the field of molecular modeling. Efforts have been made to improve accuracy and precision those calculations. One efforts is employ Hamiltonian replica exchange dynamics (H-REMD) method enhance conformational sampling. In this paper, we demonstrated that H-REMD not only improves convergence alchemical but also can be used compute differences directly via Free Energy Perturbation (FEP) algorithm. We show direct mapping between usual FEP equations, which are then energies. The calculation (replica perturbation, REFEP) was tested on predicting pKa value buried Asp26 thioredoxin. compare results REFEP with TI regular simulations. converged faster than from final pr...
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