PMID: 22587204May 17, 2012Paper

Parallel-pulling protocol for free-energy evaluation

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Van A Ngo

Abstract

Jarzynski's equality (JE) allows us to compute free-energy differences from distributions of work. In molecular dynamics simulations, the traditional way of constructing work distributions is to perform as many pulling simulations as possible. But reliable work distributions are not always produced in a finite number of simulations. The computational cost of using JE is not less than other commonly used methods such as thermodynamic integration and umbrella sampling methods. Here we first show a different proof of JE based on the idea of stepwise pulling procedures that is efficient in computing free energies by using JE. The key point in our proof is that the processes of turning on or off a harmonic potential to perform work are described by double Heaviside functions of time. We then show that the distributions of work performed by the potential can be easily generated from the distributions of a reaction coordinate along a pathway. Based on the proof, we propose sequential and parallel stepwise pulling protocols for generating work distributions that require suitable relaxation time at each pulling step. The criterion for reliable work distributions is that there must be sufficient mutual overlaps between the adjacent distr...Continue Reading

References

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Oct 12, 2010·Journal of Chemical Theory and Computation·Gungor OzerRigoberto Hernandez

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Citations

May 15, 2015·PloS One·Hailey R BureauRigoberto Hernandez
Oct 4, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Van A Ngo, Stephan Haas
Jan 9, 2014·The Journal of Physical Chemistry. B·Van A NgoStephan Haas
Mar 19, 2019·Journal of Chemical Information and Modeling·Tomasz Pieńko, Joanna Trylska

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