************ The 13th Lab Seminar **************************************

Title : Constant pH Molecular Dynamics in Explicit Solvent with 
lambda-Dynamics
Serena Donnini, Florian Tegeler, Gerrit Groenhof, and Helmut Grubmuller, 
J. Chem. Theory. Comput.,7 (2011) 1962-1978 (DOI:10.1021/ct200061r)

Speaker : Yukichi Kitamura

Date : Thu. Jan. 30th, 1:30 pm

Place : Seminar room of 4F, Graduate School of Information Science

Abstract :
pH is an important parameter in condensed-phase systems, because it 
determines the protonation state of titratable groups and thus influences 
the structure, dynamics, and function of molecules in solution. In most 
force field simulation protocols, however, the protonation state of a 
system (rather than its pH) is kept fixed and cannot adapt to changes of 
the local environment. Here, we present a method, implemented within the 
MD package GROMACS, for constant pH molecular dynamics simulations in 
explicit solvent that is based on the lambda-dynamics approach. In the 
latter, the dynamics of the titration coordinate lambda, which 
interpolates between the protonated and deprotonated states, is driven 
by generalized forces between the protonated and deprotonated states. 
The hydration free energy, as a function of pH, is included to facilitate 
constant pH simulations. The protonation states of titratable groups are 
allowed to change dynamically during a simulation, thus reproducing 
average protonation probabilities at a certain pH. The accuracy of the 
method is tested against titration curves of single amino acids and a 
dipeptide in explicit solvent.

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