TY - JOUR
T1 - Constrained molecular dynamics in the isothermal-isobaric ensemble and its adaptation for adiabatic free energy dynamics
AU - Yu, T. Q.
AU - Tuckerman, M. E.
N1 - Copyright:
Copyright 2011 Elsevier B.V., All rights reserved.
PY - 2011/11
Y1 - 2011/11
N2 - The implementation of holonomic constraints within measure-preserving integrators for molecular dynamics simulations in the isothermal-isobaric ensemble is considered. We review the basic methodology of generating measure-preserving integrators for the microcanonical, canonical, and isothermal-isobaric ensembles and proceed to show how the standard SHAKE and RATTLE algorithms must be modified for the isothermal-isobaric ensemble. Comparison is made between constrained and unconstrained simulations employing multiple time scale integration techniques. Finally, we describe a temperature accelerated version of the isothermal-isobaric molecular dynamics approach, in which the cell matrix is adiabatically decoupled from the particles and maintained at a high temperature as a means of exploring polymorphism in molecular crystals. We demonstrate that constraints can be easily adapted for this new approach and, again, we compare the performace of this temperature-accelerated scheme with and without bond constraints.
AB - The implementation of holonomic constraints within measure-preserving integrators for molecular dynamics simulations in the isothermal-isobaric ensemble is considered. We review the basic methodology of generating measure-preserving integrators for the microcanonical, canonical, and isothermal-isobaric ensembles and proceed to show how the standard SHAKE and RATTLE algorithms must be modified for the isothermal-isobaric ensemble. Comparison is made between constrained and unconstrained simulations employing multiple time scale integration techniques. Finally, we describe a temperature accelerated version of the isothermal-isobaric molecular dynamics approach, in which the cell matrix is adiabatically decoupled from the particles and maintained at a high temperature as a means of exploring polymorphism in molecular crystals. We demonstrate that constraints can be easily adapted for this new approach and, again, we compare the performace of this temperature-accelerated scheme with and without bond constraints.
UR - http://www.scopus.com/inward/record.url?scp=83355165060&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=83355165060&partnerID=8YFLogxK
U2 - 10.1140/epjst/e2011-01524-x
DO - 10.1140/epjst/e2011-01524-x
M3 - Review article
AN - SCOPUS:83355165060
SN - 1951-6355
VL - 200
SP - 183
EP - 209
JO - European Physical Journal: Special Topics
JF - European Physical Journal: Special Topics
IS - 1
ER -