It is shown that the PMD enhanced sampling approach in combination with force-field MD simulations of conformational transitions that require three or more collective variables (CVs) to describe the processes efficiently localizes the average transition path and simultaneously obtains the free-energy profile along the...
It is found that the conformation of a Trp and a Met near the flavin is crucial to modulate the rate-determining barrier, which differs significantly between the BlrB and AppA proteins.
This work employs highly efficient path-based sampling methods to perform unprecedented free-energy calculations of the base-pairing transition, and finds evidence of triple-hydrogen-bonded neighbors hindering the inside transition.
Molecular dynamics simulations are used to compute the potential of mean force (PMF) between two united-atom methane molecules at several temperatures and integration time-steps. At a fixed time-step, the contact minimum of the PMF deepens with increasing temperature, as expected for hydrophobicity driven association....
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