Protein Simulations by Multibaric–Multithermal Molecular Dynamics Algorithm

Abstract

Multibaric-multithermal molecular dynamics algorithm is reviewed. In this algorithm, twodimensional random walks not only in the potential-energy space but also in the volume space are realized. One can discuss the temperature dependence and pressure dependence of biomolecules with this algorithm. Applications to an alanine dipeptide and chignolin in explicit water solvent are also presented.

Atomistic detailed free‐energy landscape of intrinsically disordered protein studied by multi‐scale divide‐and‐conquer molecular dynamics simulation

“…As high free-energy barriers separate the minima, conventional AAM simulations suffer from a problem known as kinetic trapping. Some of GEMs, such as the replica-exchange method, [25][26][27] multibaric-multithermal method, [28][29][30][31] multi-canonical method, [32][33][34][35] Wang-Landau method, [36][37][38][39][40] and metadynamics, [41][42][43] are developed to overcome this trapping. Examples of other types of GEM include the umbrella-sampling method 44,45 and string method [46][47][48] ; the umbrella-sampling method enables sampling at a local region of reaction coordinate, whereas the string method enables sampling along reaction coordinate.…”