Constant-pH molecular dynamics simulations: a test case of succinic acid

A method for performing constant-pH molecular dynamics (MD) simulations, with an implicit solvent and explicit treatment of protonation/deprotonation phenomena, is applied to a succinic acid molecule. The protonation state of each ionizable group in the molecule is allowed to change during the MD tr...

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Bibliographic Details
Published in:Chemical physics 2004-07, Vol.302 (1), p.161-170
Main Authors: Dlugosz, Maciej, Antosiewicz, Jan M
Format: Article
Language:English
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Summary:A method for performing constant-pH molecular dynamics (MD) simulations, with an implicit solvent and explicit treatment of protonation/deprotonation phenomena, is applied to a succinic acid molecule. The protonation state of each ionizable group in the molecule is allowed to change during the MD trajectory at predefined time intervals, dividing the whole simulation into a set of sub-trajectories. Each change in the protonation state of the molecule at the beginning of a new sub-trajectory is made with a probability determined by the electrostatic free energies of the available states, based on the last structure of the preceding sub-trajectory. Our simulations resulted in the distribution of conformational states of the molecule, and in its molecular p K as, in good agreement with available experimental data. Moreover, dependence of the distribution of the trans/gauche conformers on the time interval selected for the sub-trajectories between making decisions regarding protonation states of the residues, indicates that this equilibrium is sensitive to the dynamics of proton exchange.
ISSN:0301-0104
DOI:10.1016/j.chemphys.2004.03.031