Free-energy calculations - Theoretical Biophysics Group
Free-energy calculations - Theoretical Biophysics Group
Free-energy calculations - Theoretical Biophysics Group
Create successful ePaper yourself
Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.
Reaction coordinate–based free-<strong>energy</strong> <strong>calculations</strong> Reversible unfolding of a short peptide<br />
54 PARK ET AL. (2003)<br />
55 HÉNIN, CHIPOT (2004); CHIPOT, HÉNIN (2005)<br />
Pulling of deca–alanine to investigate the equilibrium between<br />
the native, α–helical conformation and an ensemble<br />
of extended structures.<br />
Steered molecular dynamics and the application of the<br />
Jarzynski equality with a cumulant expansion: 54<br />
exp[−β ∆A(ξ)] = 〈exp[−β w(ξ)]〉<br />
Reference reversible pulling: 200.0 ns<br />
Jarzynski: 100 × 2.0 ns (v = 10.0 ˚A/ns)<br />
100 × 0.2 ns (v = 100.0 ˚A/ns)<br />
Unconstrained dynamics with the formalism of the average<br />
force. The chosen order parameter, ξ, is the distance<br />
separating the first and the last α–carbon atoms. 55<br />
Chris Chipot <strong>Free</strong>-<strong>energy</strong> <strong>calculations</strong>