A method of free energy calculation based on Jarzynski's equality and the stiff-spring approximation is presented. Thus, this is applied to an steered molecular dynamics (SMD) simulation of the helix-coil transition of deca-alanine in vacuum. It is found that when only a limited number of trajectories of irreversible processes are available, the second order cumulant expansion yields the most accurate estimate, which can be further improved by using the unbiased estimate.
ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry