Dynamics Coupled with Acid-Base Titration

MOLECULAR DYNAMICS COUPLED WITH ACID-BASE TITRATION 

1-ns simulations of hen egg lysozyme at various pH [31]. A major problem was the incorrect prediction of protonation states when the pH deviates from the expected pKa value by more than 2 units [31]. 

In the hybrid Hamiltonian, the charge states and van der Waals parameters involving titrating side chains are linearly attenuated by the values of A, fhereby enabling a coupling between conformational and protonation dynamics. The biasing potential is defined as 

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Static Structure Based pK Prediction Methods Molecular Dynamics Coupled with Acid-Base Titration... 

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