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Often gaining insight into the functioning of biomolecular systems requiresto follow their dynamics along a microscopic reaction coordinate (RC) on amacroscopic time scale, which is beyond the reach of current all atom moleculardynamics (MD) simulations. A practical approach to this inherently multiscaleproblem is to model the system as a fictitious overdamped Brownian particlethat diffuses along the RC in the presence of an effective potential of meanforce (PMF) due to the rest of the system. By employing the recently proposedFR method [I. Kosztin et al., J. of Chem. Phys. 124, 064106 (2006)], whichrequires only a small number of fast nonequilibrium MD simulations of thesystem in both forward and time reversed directions along the RC, wereconstruct the PMF: (1) of deca-alanine as a function of its end-to-enddistance, and (2) that guides the motion of potassium ions through thegramicidin A channel. In both cases the computed PMFs are found to be in goodagreement with previous results obtained by different methods. Our approachappears to be about one order of magnitude faster than the other PMFcalculation methods and, in addition, it also provides the position dependentdiffusion coefficient along the RC. Thus, the obtained PMF and diffusioncoefficient can be used in a suitable stochastic model to estimate importantcharacteristics of the studied systems, e.g., the mean folding time of thestretched deca-alanine and the mean diffusion time of the potassium ion throughgramicidin A.

Calculating free energy profiles in biomolecular systems from fast non-equilibrium processes