TY - JOUR
T1 - Recent applications of boxed molecular dynamics
T2 - A simple multiscale technique for atomistic simulations
AU - Booth, Jonathan
AU - Vazquez, Saulo
AU - Martinez-Nunez, Emilio
AU - Marks, Alison
AU - Rodgers, Jeff
AU - Glowacki, David R.
AU - Shalashilin, Dmitrii V.
PY - 2014/8/6
Y1 - 2014/8/6
N2 - 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 othermethods of acceleratedMD
AB - 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 othermethods of acceleratedMD
KW - Chemical dynamics
KW - Dynamics of proteins
KW - Kinetics
KW - Molecular dynamics
KW - Quantum mechanics
UR - http://www.scopus.com/inward/record.url?scp=84903977723&partnerID=8YFLogxK
U2 - 10.1098/rsta.2013.0384
DO - 10.1098/rsta.2013.0384
M3 - Article (Academic Journal)
C2 - 24982247
AN - SCOPUS:84903977723
VL - 372
SP - 1
EP - 13
JO - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
JF - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
SN - 1364-503X
IS - 2021
M1 - 20130384
ER -