Paper Citing NAMD - Abstract
Park, S.; Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K.
Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
JOURNAL OF CHEMICAL PHYSICS, 119:3559-3566, AUG 8 2003
Jarzynski's equality is applied to free energy calculations from steered molecular dynamics simulations of biomolecules. The helix-coil transition of deca-alanine in vacuum is used as an example. With about ten trajectories sampled, the second order cumulant expansion, among the various averaging schemes examined, yields the most accurate estimates. We compare umbrella sampling and the present method, and find that their efficiencies are comparable. (C) 2003 American Institute of Physics.
