Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules.
J Comput Chem
; 35(1): 39-50, 2014 Jan 05.
Article
en En
| MEDLINE
| ID: mdl-24166005
ABSTRACT
A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems.
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Oligopéptidos
/
Polilisina
/
Simulación de Dinámica Molecular
Idioma:
En
Revista:
J Comput Chem
Asunto de la revista:
QUIMICA
Año:
2014
Tipo del documento:
Article
País de afiliación:
Japón