Steered molecular dynamics can provide a view of what happens to a molecule or protein as one literally moves atoms or fragments of the molecule toward or away from each other. As such motions are often rare events, the external artifice of steering allows for a much larger sampling of such structures than would be seen using standard statistical weights. Moreover, through the use of nonequilibrium work theorems, such as that of Jarzynkski and Crooks, one can formally obtain the correctly averaged free energy difference along such a path. The convergence, of these expressions, can fail for long paths, however. We have developed the adaptive steered molecular dynamics (ASMD) approach to circumvent this obstacle by way of introducing stages in which the trajectories are literally or effectively relaxed. The efficacy of the method will be illustrated using decaalanine and several other small to mid-size peptides. In recognition of the ACS Award for Encouraging Disadvantaged Students into Careers in the Chemical Sciences, I will conclude with a discussion of policies and procedures that can be implemented in chemistry departments to ensure that the sampling leading to future faculty is equitable and diverse.

Award Address  (ACS Award for Encouraging Disadvantaged Students into Careers in the Chemical Sciences sponsored by The Camille and Henry Dreyfus Foundation, Inc.). Optimizing the sampling of nonequilibrium trajectories and careers

247th National Meeting (2014)

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