Eur. Phys. J. Special Topics 200, 183-209 (2011)
https://doi.org/10.1140/epjst/e2011-01524-x

Review

Constrained molecular dynamics in the isothermal-isobaric ensemble and its adaptation for adiabatic free energy dynamics

¹ Department of Chemistry, New York University, New York, NY 10003, USA
² Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, USA

^a e-mail: tqy200@nyu.edu
^b e-mail: mark.tuckerman@nyu.edu

Received: 9 September 2011
Revised: 10 October 2011
Published online: 13 December 2011

Abstract

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.