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.

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations / Marsili, Simone; Barducci, Alessandro; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo. - In: JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL. - ISSN 1520-6106. - STAMPA. - 110:(2006), pp. 14011-14013. [10.1021/jp062755j]

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations

CHELLI, RICCARDO;PROCACCI, PIERO;SCHETTINO, VINCENZO
2006

Abstract

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.
2006
110
14011
14013
Marsili, Simone; Barducci, Alessandro; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo
File in questo prodotto:
File Dimensione Formato  
J.Phys.Chem.B-y06_v110_p14011.pdf

Accesso chiuso

Descrizione: Articolo principale
Tipologia: Pdf editoriale (Version of record)
Licenza: Tutti i diritti riservati
Dimensione 158.5 kB
Formato Adobe PDF
158.5 kB Adobe PDF   Richiedi una copia

I documenti in FLORE sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/370542
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 116
  • ???jsp.display-item.citation.isi??? 108
social impact