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
Revised: 10 October 2011
Published online: 13 December 2011
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.
© EDP Sciences, Springer-Verlag, 2011