Molecular dynamics (MD) offers the unprecedented ability to observe the physical and structural dynamics of biomolecules as they move in nature. As the computational cost associated with this modeling has decreased and the potential it harbors has been recognized, there has been a hard push to incorporate dynamic information into the drug discovery pathway. The ability to perform MD on both a rapid and cost-effective platform has greatly increased the feasibility of routinely incorporating dynamic studies into what was once a purely static viewpoint.  However, looking at protein structure only shows us half the picture. Solvation dynamics in a biomolecular context has been shown repeatedly to play a critical role in any number of processes, from ligand binding, to protein conformational dynamics, to catalysis and protein-protein interactions. It is of import to understand the conditions which lead most directly to a converged solvation structure; to that end GPU-accelerated molecular dynamics has been applied to a range of diverse targets at superfine trajectory print rates and then analyzed using the WATMD method. This allows us to determine which combination of print rate and simulation length results in the most computationally cost-effective solvation convergence. Furthermore, using these methods we were able to determine the convergence rates for highly organized water, relative to moderately organized waters or bulk. The goal is to allow not only protein structure and dynamics to guide the future of drug design, but to utilize the salient features of the solvation structure as well.

Convergence of solvation structure in superfine print molecular dynamics

248th National Meeting (2014)

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