# Symplectic algorithm for constant-pressure molecular dynamics using a Nosé–Poincaré thermostat

@article{Sturgeon2000SymplecticAF, title={Symplectic algorithm for constant-pressure molecular dynamics using a Nos{\'e}–Poincar{\'e} thermostat}, author={Jess B. Sturgeon and Brian B. Laird}, journal={Journal of Chemical Physics}, year={2000}, volume={112}, pages={3474-3482} }

We present a new algorithm for isothermal–isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nose–Poincare thermostat, recently developed by Bond, Leimkuhler, and Laird [J. Comp. Phys. 151, 114 (1999)]. This Nose–Poincare–Andersen (NPA) formulation has advantages over the Nose-Hoover-Andersen approach in that the NPA is Hamiltonian and can take advantage of symplectic integration schemes, which lead to enhanced stability for…

## 21 Citations

### MOLECULAR SIMULATION IN THE CANONICAL ENSEMBLE AND BEYOND

- Engineering
- 2007

In this paper, we discuss advanced thermostatting techniques for sampling molecular systems in the canonical ensemble. We first survey work on dynamical thermostatting methods, including the…

### Hamiltonian thermostatting techniques for molecular dynamics simulation

- Physics
- 2004

Hamiltonian Thermostatting Techniques for Molecular Dynamics Simulation. Molecular dynamics trajectories that sample from a Gibbs, or canonical, distribution can be generated by introducing a…

### Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator

- Environmental Science
- 2010

### A Hamiltonian Formulation for Recursive Multiple Thermostats in a Common Timescale

- PhysicsSIAM J. Appl. Dyn. Syst.
- 2005

A new powerful "recursive thermostatting" procedure is proposed which obtains canonical sampling without the stability problems encountered with Nose-Hoover and Nose-Poincare chains.

### The canonical ensemble via symplectic integrators using Nosé and Nosé-Poincaré chains.

- MathematicsThe Journal of chemical physics
- 2004

A method is proposed whereby additional thermostats can be applied to a Hamiltonian system while retaining sampling from the canonical ensemble, used to construct thermostatting chains for the Nosé and Nosé-Poincaré methods.

### A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal?isobaric ensemble

- Physics
- 2006

The constant-pressure, constant-temperature (NPT) molecular dynamics approach is re-examined from the viewpoint of deriving a new measure-preserving reversible geometric integrator for the equations…

### Metric-tensor flexible-cell algorithm for isothermal–isobaric molecular dynamics simulations

- Physics
- 2001

An extended Hamiltonian approach to conduct isothermal–isobaric molecular dynamics simulations with full cell flexibility is proposed. The components of the metric tensor are used as the fictitious…

### A novel method for molecular dynamics simulation in the isothermal–isobaric ensemble

- Physics
- 2011

A novel algorithm is proposed to study fluid properties in the isothermal–isobaric (NPT) ensemble. The major feature of this approach is that the constant pressure in the NPT ensemble is created by…

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

- Chemistry
- 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…

### Simple algorithm for isothermal–isobaric molecular dynamics

- PhysicsJ. Comput. Chem.
- 2004

The principles of non‐Hamiltonian statistical mechanics are reviewed and a new set of equations and integration algorithm for isothermal–isobaric dynamics is presented that is somewhat simpler than previous methods.

## References

SHOWING 1-10 OF 40 REFERENCES

### The Nosé-Poincaré Method for Constant Temperature Molecular Dynamics

- Physics
- 1999

We present a new extended phase space method for constant temperature (canonical ensemble) molecular dynamics. Our starting point is the Hamiltonian introduced by Nose to generate trajectories…

### A unified formulation of the constant temperature molecular dynamics methods

- Physics, Chemistry
- 1984

Three recently proposed constant temperature molecular dynamics methods by: (i) Nose (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss [Chem.…

### Molecular dynamics simulations at constant pressure and/or temperature

- Physics
- 1980

In the molecular dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed volume are solved numerically. The energy, volume, and number of particles are…

### Isothermal molecular-dynamics ensembles.

- PhysicsPhysical review. A, General physics
- 1988

It is shown that Nose’s theory can be modified so that it generates phase-space trajectories corresponding to a constant-momentum canonical ensemble with zero total momentum, including expressions relating averages to thermodynamic variables and formulas involving thermodynamic response functions which are often used in molecular-dynamics calculations.

### Canonical dynamics: Equilibrium phase-space distributions.

- PhysicsPhysical review. A, General physics
- 1985

The dynamical steady-state probability density is found in an extended phase space with variables x, p/sub x/, V, epsilon-dot, and zeta, where the x are reduced distances and the two variables epsilus-dot andZeta act as thermodynamic friction coefficients.

### Constant Temperature Molecular Dynamics Methods

- Physics
- 1991

How the canonical distribution is realized in simulations based on deterministic dynamical equations is explained in this review. Basic formulations and their recent extensions of two constant…

### A molecular dynamics method for simulations in the canonical ensemble

- Physics, Chemistry
- 1984

A molecular dynamics simulation method which can generate configurations belonging to the canonical (T, V, N) ensemble or the constant temperature constant pressure (T, P, N) ensemble, is proposed.…

### A comparison of constant energy, constant temperature and constant pressure ensembles in molecular dynamics simulations of atomic liquids

- Chemistry, Physics
- 1984

Dynamic and static properties of the LJ fluid at a density and temperature close to the triple point are determined and compared for molecular dynamics computer simulations using (N, V, E), (N, V,…

### Numerical Hamiltonian Problems

- Computer Science, Mathematics
- 1994

Examples of Hamiltonian Systems, symplectic integration, and Numerical Methods: Checking preservation of area: Jacobians, and Necessity of the symplecticness conditions.

### Explicit reversible integrators for extended systems dynamics

- Computer Science
- 1996

Explicit reversible integrators, suitable for use in large-scale computer simulations, are derived for extended systems generating the canonical and isothermal-isobaric ensembles. The new methods are…