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Journal of Chemical Theory and Computation
Article . 2010 . Peer-reviewed
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Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

Authors: Williams, Sarah L; de Oliveira, César Augusto F; McCammon, J Andrew;

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

Abstract

An extension of the constant pH method originally implemented by Mongan et al. (J. Comput. Chem.2004, 25, 2038-2048) is proposed in this study. This adapted version of the method couples the constant pH methodology with the enhanced sampling technique of accelerated molecular dynamics, in an attempt to overcome the sampling issues encountered with current standard constant pH molecular dynamics methods. Although good results were reported by Mongan et al. on application of the standard method to the hen egg-white lysozyme (HEWL) system, residues which possess strong interactions with neighboring groups tend to converge slowly, resulting in the reported inconsistencies for predicted pK(a) values, as highlighted by the authors. The application of the coupled method described in this study to the HEWL system displays improvements over the standard version of the method, with the improved sampling leading to faster convergence and producing pK(a) values in closer agreement to those obtained experimentally for the more slowly converging residues.

Keywords

Computer Software, Chemical Physics, Physical chemistry, Theoretical and Computational Chemistry, Theoretical and computational chemistry, Chemical Sciences, Biochemistry and Cell Biology, 540

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
91
Top 10%
Top 10%
Top 10%
Green
hybrid