Molecular Dynamics-style simulations used to be done in vacuo, then in dielectric media and only later on in real water. They were also at constant energy, until thermostats and barostats came to the fore. In this talk, I will highlight our methods to to get closer and closer to experimental conditions, in this case, simulating pH and electrochemical potentials. I will show what the method can do, specially when coupled to replica exchange. We have very recently ported the whole method to GPUs inside the amber package, and can now perform constant pH simulations at basically the same computational cost as regular MD. <br/><br/>These advances open doors for the study of several system such as pH switches, enzyme structure, function and dynamics. In particular, they create interesting questions regarding the meaning of pKas and conformational energies in complex systems.

Constant pH simulations in biomolecular systems

251st National Meeting (2016)

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