^{1}and Dušanka Janežič

^{1,a)}

### Abstract

The new symplectic molecular dynamics (MD) integrators presented in the first paper of this series were applied to perform MD simulations of water. The physical properties of a system of flexible TIP3P water molecules computed by the new integrators, such as diffusion coefficients, orientation correlation times, and infrared (IR) spectra, are in good agreement with results obtained by the standard method. The comparison between the new integrators’ and the standard method’s integration time step sizes indicates that the resulting algorithm allows a long integration time step as opposed to the standard leap-frog Verlet method, a sixfold simulation speed-up. The accuracy of the method was confirmed, in particular, by computing the IR spectrum of water in which no blueshifting of the stretching normal mode frequencies is observed as occurs with the standard method.

The authors thank Dr. M. Hodošček and Dr. F. Merzel for helpful discussions and to U. Borštnik for careful reading of the manuscript. This work was supported by the Ministry of Education, Science and Sports of Slovenia under Grant Nos. P1-0002 and J1-6331.

I. INTRODUCTION

II. METHODS

A. Overview of integration methods

B. Diffusion coefficient

C. Orientational correlation times

D. IR spectrum

III. COMPUTATIONAL DETAILS

A. Water model

B. Vibrational potential energy and internal coordinate system

C. Simulation protocol

IV. RESULTS AND DISCUSSION

A. Structural properties

1. Radial distribution functions

B. Dynamical properties

1. Diffusion coefficient

2. Orientational correlation times

C. IR spectrum

V. CONCLUSIONS

### Key Topics

- Infrared spectra
- 30.0
- Diffusion
- 21.0
- Molecular dynamics
- 16.0
- Infrared molecular spectra
- 13.0
- Molecular spectra
- 13.0

## Figures

Description of the positions of atoms in the equilibrium configuration of a water molecule. The orthogonal unit vectors and are the two unit vectors, which define the internal coordinate system of a molecule.

Description of the positions of atoms in the equilibrium configuration of a water molecule. The orthogonal unit vectors and are the two unit vectors, which define the internal coordinate system of a molecule.

(a) Error in the total energy of the system of 256 water molecules with at using the LFV, SISM, and SISM-MTS for . (b) Error in total energy of the system of 256 water molecules with at using the LFV-EQ, SISM-EQ, and SISM-MTS-EQ for .

(a) Error in the total energy of the system of 256 water molecules with at using the LFV, SISM, and SISM-MTS for . (b) Error in total energy of the system of 256 water molecules with at using the LFV-EQ, SISM-EQ, and SISM-MTS-EQ for .

(Color) IR spectrum (arbitrary units) of bulk water at calculated by LFV, SISM, and SISM-MTS using an integration time step of (a) and (b) .

(Color) IR spectrum (arbitrary units) of bulk water at calculated by LFV, SISM, and SISM-MTS using an integration time step of (a) and (b) .

(Color) IR spectrum (arbitrary units) of bulk water at calculated by LFV, SISM, and SISM-MTS using an integration time step of (a) and (b) .

(Color) IR spectrum (arbitrary units) of bulk water at calculated by LFV-EQ, SISM-EQ, and SISM-MTS-EQ using an integration time step of (a) and (b) .

(Color) IR spectrum (arbitrary units) of bulk water at calculated by LFV-EQ, SISM-EQ, and SISM-MTS-EQ using an integration time step of (a) and (b) .

## Tables

Parameters of the flexible TIP3P model of the molecule (Refs. 18 and 19). The quantity is the elementary charge.

Parameters of the flexible TIP3P model of the molecule (Refs. 18 and 19). The quantity is the elementary charge.

Experimental vibrational frequencies of the molecule (Ref. 47) and normal mode frequencies of the molecule determined by normal mode analysis using parameters from Table I.

Experimental vibrational frequencies of the molecule (Ref. 47) and normal mode frequencies of the molecule determined by normal mode analysis using parameters from Table I.

Comparison of , , and calculated by the LFV, SISM, and SISM-MTS. We give the positions and heights of the first maximum of the calculated functions and the corresponding experimental values (Ref. 42).

Comparison of , , and calculated by the LFV, SISM, and SISM-MTS. We give the positions and heights of the first maximum of the calculated functions and the corresponding experimental values (Ref. 42).

Comparison of , , and calculated by the LFV-EQ, SISM-EQ, and SISM-MTS-EQ. We give the positions and heights of the first maximum of the calculated functions and the corresponding experimental values (Ref. 42).

Comparison of , , and calculated by the LFV-EQ, SISM-EQ, and SISM-MTS-EQ. We give the positions and heights of the first maximum of the calculated functions and the corresponding experimental values (Ref. 42).

Diffusion coefficient for the system of 256 flexible TIP3P water molecules calculated using Eq. (3) (MSD) and Eq. (1) (VAC) and various integration time steps. Experimental value of for liquid water at is (Ref. 37).

Diffusion coefficient for the system of 256 flexible TIP3P water molecules calculated using Eq. (3) (MSD) and Eq. (1) (VAC) and various integration time steps. Experimental value of for liquid water at is (Ref. 37).

Diffusion coefficient for the system of 256 flexible TIP3P water molecules calculated using Eq. (3) (MSD) and Eq. (1) (VAC) and various integration time steps. Experimental value of for liquid water at is (Ref. 37).

Orientational correlation times for the system of 256 flexible TIP3P water molecules at obtained by using various integration time steps. The corresponding experimental values of at are (Ref. 48), (Ref. 24), (Ref. 43).

Orientational correlation times for the system of 256 flexible TIP3P water molecules at obtained by using various integration time steps. The corresponding experimental values of at are (Ref. 48), (Ref. 24), (Ref. 43).

Orientational correlation times for the system of 256 flexible TIP3P water molecules at obtained by using various integration time steps. The corresponding experimental values of at are (Ref. 48), (Ref. 24), (Ref. 43).

Article metrics loading...

Full text loading...

Commenting has been disabled for this content