Adaptive conformational sampling based on replicas |
| |
Authors: | Jeremy Curuksu |
| |
Institution: | 1. Institute of Mathematics, Ecole Polytechnique Fédérale de Lausanne (EPFL), MATHGEOM, LCVMM, Station 8, MAC1 615, 1015, Lausanne, Switzerland
|
| |
Abstract: | Computer simulations of biomolecules such as molecular dynamics simulations are limited by the time scale of conformational
rearrangements. Several sampling techniques are available to search the multi-minima free energy landscape but most efficient,
time-dependent methods do generally not produce a canonical ensemble. A sampling algorithm based on a self-regulating ladder
of searching copies in the dihedral subspace is developped in this paper. The learning process using short- and long-term
memory functions allows an efficient search in phase space while combining a deterministic dynamics and stochastic swaps with
the searching copies conserves a canonical limit. The sampling efficiency and accuracy are indicated by comparing the ansatz
with conventional molecular dynamics and replica exchange simulations. |
| |
Keywords: | |
本文献已被 PubMed SpringerLink 等数据库收录! |
|