Abstract
This paper proposes a new approach to the time-scale problem in molecular dynamics (MD) simulations that allows to accelerate the dynamical processes and to describe the dynamics on the correct time scale under time reparameterization. The scheme is general and can be applied to a variety of systems from device materials to biomolecules.
Highlights
Molecular dynamics (MD) simulations have been recognized as one of the most powerful tools for investigating dynamical processes at an atomistic level, such as impurity diffusion in a crystal and protein conformational changes
We have introduced an alternative approach, Poincaré boost dynamics (PBD), to tackle the timescale problem in molecular dynamics simulations
In order to estimate the correct timescale of the dynamical events induced in biased MD runs, we utilized a generalized version of the Poincaré time transformation
Summary
Molecular dynamics (MD) simulations have been recognized as one of the most powerful tools for investigating dynamical processes at an atomistic level, such as impurity diffusion in a crystal and protein conformational changes. A variety of biased sampling techniques have been introduced in MD simulations, such as multicanonical MD [5,6,7], accelerated MD [8,9], and Tsallis dynamics [10,11,12], to increase the rate of overcoming the barriers and to sample such events more frequently To this end, a bias potential function is introduced in addition to the original potential of , leading to the sampling of the distribution of exp[−β( + )], i.e., biased sampling. Voter introduced hyperdynamics [13,14] that allows for accelerating the sampling of the infrequent events and for estimating the original timescale of these events (such as escape rates for stable states) This is, based on transition state theory (TST) [15]; the method can only be applied to specific systems where the dynamical processes can be described by TST well.
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