Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.
Philos Trans A Math Phys Eng Sci
; 372(2021)2014 Aug 06.
Article
in En
| MEDLINE
| ID: mdl-24982247
ABSTRACT
In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Biopolymers
/
Algorithms
/
Molecular Dynamics Simulation
/
Models, Chemical
Language:
En
Journal:
Philos Trans A Math Phys Eng Sci
Journal subject:
BIOFISICA
/
ENGENHARIA BIOMEDICA
Year:
2014
Document type:
Article
Affiliation country:
Reino Unido