Accelerating Molecular Dynamics Simulations with Population Annealing
نویسندگان
چکیده
منابع مشابه
Accelerating Molecular Dynamics Simulations with GPUs
Molecular dynamics simulations are known to run for many days or weeks before completion. In this paper we explore the use of GPUs to accelerate a LennardJones-based molecular dynamics simulation of up to 27000 atoms. We demonstrate speedups that exceed 100x on commodity Nvidia GPUs and discuss the strategies that allow for such exceptional speedups. We show that traditional molecular dynamics ...
متن کاملAccelerating molecular dynamics simulations by linear prediction of time series
We present a molecular dynamics simulation scheme which allows to speed up molecular dynamics simulations by linear prediction of force time series. The explicit calculation of nonbonding forces is periodically replaced by linear prediction from past values. Applying our method to liquid oxygen consisting of flexible molecules we obtained real speedups between 5.4 and 6.5, compared to conventio...
متن کاملAccelerating Fermionic Molecular Dynamics
For over fifteen years the algorithm of choice for generating lattice field theory configurations including the dynamical effect of fermions has been Hybrid Monte Carlo (HMC) [1]. Unfortunately the cost of this algorithm increases rapidly as the fermion mass m decreases; in order to keep the HMC acceptance rate Pacc constant the molecular dynamics integration step size δτ has to be reduced, and...
متن کاملAnnealing schedule from population dynamics
Population-based optimization algorithms [1–3] have been successfully applied to problems in physics [4,5] and beyond [6]. This class of algorithms is based on the simultaneous tracking of more than one point in search space (a “population”, in analogy to biological evolution [7]), in order to make trapping in local optima less likely during the process of optimization. In addition, stochastic ...
متن کاملMolecular dynamics simulations.
Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible. Simulations aid our understanding of biochemical processe...
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: Physical Review Letters
سال: 2019
ISSN: 0031-9007,1079-7114
DOI: 10.1103/physrevlett.122.060602