Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations.
We propose a new approach for the umbrella sampling method in molecular dynamics simulations of complex systems. An accelerated sampling of the slow degrees of freedom is achieved by generating a single self-adaptive trajectory that tends to span uniformly the reaction coordinate using a time dependent bias potential derived from the preceding history of the system. To show the convergent behavior and the efficiency of the method, we present the free energy surface of alanine dipeptide in water as a function of the backbone dihedral angles.
Marsili
Simone
S
Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy.
Barducci
Alessandro
A
Chelli
Riccardo
R
Procacci
Piero
P
Schettino
Vincenzo
V