J. Chem. Phys. Abstract
Abstract
In this paper (paper I) and a companion paper (paper II),
novel new algorithms and applications of the
isokinetic ensemble as generated by Gauss' principle of least
constraint, pioneered for use with molecular dynamics
twenty years ago, are presented for biophysical, path integral,
and Car-Parrinello based ab initio molecular dynamics.
In paper I, a new
``extended system'' version of the isokinetic equations of motion
that overcomes the ergodicity problems inherent in the standard approach,
is developed using a new theory of non-Hamiltonian phase space analysis
[M. E. Tuckerman, et al., Europhys. Lett.
45, 149 (1999);
M. E. Tuckerman, et al., J. Chem. Phys. 115, (2001)].
Reversible multiple time step integrations schemes for the isokinetic
methods, first presented by Zhang
[J. Chem. Phys. 106, 6102 (1997)] are reviewed.
Next, holonomic constraints
are incorporated into the isokinetic methodology
for use in fast efficient biomolecular simulation studies.
Model and realistic examples are presented in order to
evaluate, critically, the performance of the new isokinetic molecular dynamics schemes.
Comparisons are made to, the now
standard, canonical dynamics method, Nosé-Hoover chain dynamics
[G. J. Martyna, et al., J. Chem. Phys. 97,
2635 (1992)].
The new isokinetic techniques are found to yield more efficient sampling
than the Nosé-Hoover chain method in both path integral molecular dynamics and biophysical
molecular dynamics calculations.
In paper II, the use of isokinetic methods in Car-Parrinello based
ab initio
molecular dynamics calculations is presented.