Optimal allocation of replicas in parallel tempering simulations
نویسندگان
چکیده
منابع مشابه
Optimal Allocation of Replicas to Processors in Parallel Tempering Simulations
The optimal allocation of replicas to a homogeneous or heterogenous set of processors is derived for parallel tempering simulations on multi-processor machines. In the general case, it is possible without substantially increasing wall clock time to achieve nearly perfect utilization of CPU time. Random fluctuations in the execution times of each of the replicas do not significantly degrade the ...
متن کاملDynamics and optimal number of replicas in parallel tempering simulations.
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the control parameter discretization allow a treatment independent of the system in question. By analyzing mean first passage times across the control parameter ...
متن کاملOn Dynamics and Optimal Number of Replicas in Parallel Tempering Simulations
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the control parameter discretization allow a treatment independent of the system in question. Analyzing mean first passage times across control parameter space, ...
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We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins...
متن کاملOptimized parallel tempering simulations of proteins.
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an optimal set of temperatures/replicas which are found to concentrate at the bottlenecks of the simulations. A measure of convergence for the equilibration of the pa...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2005
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.1831273