Replica State Exchange Metadynamics for Improving the Convergence of Free Energy Estimates
نویسندگان
چکیده
منابع مشابه
Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.
Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force mole...
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Replica exchange molecular dynamics (REMD) method is one of the generalized-ensemble algorithms which performs random walk in energy space and helps a system to escape from local energy traps. In this work, we studied the accuracy and efficiency of REMD by examining its ability to reproduce the results of multiple extended conventional molecular dynamics (MD) simulations and to enhance conforma...
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Improving replica exchange using driven scaling.
Replica exchange is a powerful simulation method in which simulations are run at a series of temperatures, with the highest temperature chosen so phase space can be sampled efficiently. In order for swaps to be accepted, the energy distributions of adjacent replicas must have some overlap. This can create the need for many replicas for large systems. In this paper, we present a new method in wh...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2016
ISSN: 0192-8651
DOI: 10.1002/jcc.24338