Fig. 1.

A Schematic representation of the D-NEMD approach. The stationary (e.g., equilibrium) MD trajectory (blue line) provides the initial distribution for the nonequilibrium simulations at time t$=$0 (orange lines). The individual nonequilibrium trajectories sample the dynamic evolution of the system after the introduction of a perturbation. B Scheme for extracting the structural response of a protein to a perturbation. For each pair of stationary and nonequilibrium trajectories, the system’s response to the perturbation is obtained by comparing the position of each individual C$\mathrm{\alpha }$ atom in both trajectories at equivalent points in time. The statistical average of the response as a function of the time is then determined, and the corresponding statistical errors calculated