title: Combining path-breaking with bidirectional nonequilibrium simulations to improve efficiency in free energy calculations.
abstract: An important limitation of unidirectional nonequilibrium simulations is the amount of realizations of the process necessary to reach suitable convergence of free energy estimates via Jarzynski's relationship [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. To this regard, an improvement of the method has been achieved by means of path-breaking schemes [R. Chelli et al., J. Chem. Phys. 138, 214109 (2013)] based on stopping highly dissipative trajectories before their normal end, under the founded assumption that such trajectories contribute marginally to the work exponential averages. Here, we combine the path-breaking scheme, called probability threshold scheme, to bidirectional nonequilibrium methods for free energy calculations [G. E. Crooks, Phys. Rev. E 61, 2361 (2000); R. Chelli and P. Procacci, Phys. Chem. Chem. Phys. 11, 1152 (2009)]. The method is illustrated and tested on a benchmark system, i.e., the helix-coil transition of deca-alanine. By using path-breaking in our test system, the computer time needed to carry out a series of nonequilibrium trajectories can be reduced up to a factor 4, with marginal loss of accuracy in free energy estimates.
authors: Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy and European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
authors: Edoardo
authors: E
authors: Giovannelli
authors: Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy and European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
authors: Cristina
authors: C
authors: Gellini
authors: Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy and European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
authors: Giangaetano
authors: G
authors: Pietraperzia
authors: Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy and European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
authors: Gianni
authors: G
authors: Cardini
authors: Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy and European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy.
authors: Riccardo
authors: R
authors: Chelli