Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms
نویسندگان
چکیده
منابع مشابه
Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.
Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of...
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We discuss the use of a Langevin equation with a colored (correlated) noise to perform constanttemperature molecular dynamics simulations. Since the equations of motion are linear in nature, it is easy to predict the response of a Hamiltonian system to such a thermostat and to tune at will the relaxation time of modes of different frequency. This allows one to optimize the time needed to therma...
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The replica exchange statistical temperature molecular dynamics (RESTMD) algorithm is presented, designed to alleviate an extensive increase of the number of replicas required as system size increases in the conventional temperature replica exchange method (tREM), and to obtain improved sampling in individual replicas. RESTMD optimally integrates multiple STMD (Phys. Rev. Lett. 2006, 97, 050601...
متن کاملMolecular Dynamics Simulations using Temperature Enhanced Essential dynamics Replica EXchange (TEE-REX)
Todays standard molecular dynamics (MD) simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large numbe...
متن کاملAsynchronous replica exchange for molecular simulations
An asynchronous implementation of the replica exchange method that addresses some of the limitations of conventional synchronous replica exchange implementations is presented. In asynchronous replica exchange pairs of processors initiate and perform temperature replica exchanges independently from the other processors, thereby removing the need for processor synchronization found in conventiona...
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ژورنال
عنوان ژورنال: Journal of the Physical Society of Japan
سال: 2010
ISSN: 0031-9015,1347-4073
DOI: 10.1143/jpsj.79.074001