Molecular Dynamics Simulations Using Temperature-Enhanced Essential Dynamics Replica Exchange
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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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...
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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...
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The folding process of the 20 residue Trp-cage mini-protein was investigated using standard temperature replica exchange molecular dynamics (T-RexMD) simulation and a biasing potential RexMD (BP-RexMD) method. In contrast to several conventional molecular dynamics simulations, both RexMD methods sampled conformations close to the native structure after 10-20 ns simulation time as the dominant c...
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We review a selection of methods for performing enhanced sampling in 1 molecular dynamics simulations. We consider methods based on collective variable biasing 2 and on tempering, and offer both historical and contemporary perspectives. In collective3 variable biasing, we first discuss methods stemming from thermodynamic integration that 4 use mean force biasing, including the adaptive biasing ...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2007
ISSN: 0006-3495
DOI: 10.1529/biophysj.106.103101