On the improvement of free-energy calculation from steered molecular dynamics simulations using adaptive stochastic perturbation protocols.

ABSTRACT: The potential of mean force (PMF) calculation in single molecule manipulation experiments performed via the steered molecular dynamics (SMD) technique is a computationally very demanding task because the analyzed system has to be perturbed very slowly to be kept close to equilibrium. Faster perturbations, far from equilibrium, increase dissipation and move the average work away from the underlying free energy profile, and thus introduce a bias into the PMF estimate. The Jarzynski equality offers a way to overcome the bias problem by being able to produce an exact estimate of the free energy difference, regardless of the perturbation regime. However, with a limited number of samples and high dissipation the Jarzynski equality also introduces a bias. In our previous work, based on the Browni

SUBMITTER: Perisic O 

PROVIDER: S-EPMC4169427 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature