Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

Comparison of simple potential functions for simulating liquid water

In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath

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Molecular dynamics with coupling to an external bath.

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

http://www2.stat.duke.edu/~scs/Courses/Stat376/Papers/Constraints/Shake1977.pdf

Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

Crystal structure and pair potentials: A molecular-dynamics study

A system of 864 particles interacting with a Lennard-Jones potential and obeying classical equations of motion has been studied on a digital computer (CDC 3600) to simulate molecular dynamics in liquid argon at 94.4\ifmmode^\circ\else\textdegree\fi{}K and a density of 1.374 g ${\mathrm{cm}}^{\ensuremath{-}3}$. The pair-correlation function and the constant of self-diffusion are found to agree well with experiment; the latter is 15% lower than the experimental value. The spectrum of the velocity autocorrelation function shows a broad maximum in the frequency region $\ensuremath{\omega}=0.25(\frac{{k}_{B}T}{\ensuremath{\hbar}})$. The shape of the Van Hove function ${G}_{s}(r, t)$ attains a maximum departure from a Gaussian at about $t=3.0\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}12}$ sec and becomes a Gaussian again at about ${10}^{\ensuremath{-}11}$ sec. The Van Hove function ${G}_{d}(r, t)$ has been compared with the convolution approximation of Vineyard, showing that this approximation gives a too rapid decay of ${G}_{d}(r, t)$ with time. A delayed-convolution approximation has been suggested which gives a better fit with ${G}_{d}(r, t)$; this delayed convolution makes ${G}_{d}(r, t)$ decay as ${t}^{4}$ at short times and as $t$ at long times.

Correlations in the Motion of Atoms in Liquid Argon

Molecular dynamics calculations on a classical model for liquid water have been carried out at mass density 1 g/cm3 and at four temperatures. The effective pair potential employed is based on a four‐charge model for each molecule and represents a modification of the prior ``BNS'' interaction. Results for molecular structure and thermodynamic properties indicate that the modification improves the fidelity of the molecular dynamics simulation. In particular, the present version leads to a density maximum near 27°C for the liquid in coexistence with its vapor and to molecular distribution functions in better agreement with x‐ray scattering experiments.

Improved simulation of liquid water by molecular dynamics

A sample of water, consisting of 216 rigid molecules at mass density 1 gm/cm3, has been simulated by computer using the molecular dynamics technique. The system evolves in time by the laws of classical dynamics, subject to an effective pair potential that incorporates the principal structural effects of many‐body interactions in real water. Both static structural properties and the kinetic behavior have been examined in considerable detail for a dynamics ``run'' at nominal temperature 34.3°C. In those few cases where direct comparisons with experiment can be made, agreement is moderately good; a simple energy rescaling of the potential (using the factor 1.06) however improves the closeness of agreement considerably. A sequence of stereoscopic pictures of the system's intermediate configurations reinforces conclusions inferred from the various ``run'' averages: (a) The liquid structure consists of a highly strained random hydrogen‐bond network which bears little structural resemblance to known aqueous crys...

Molecular Dynamics Study of Liquid Water

Using a flexible version of a rigid-molecule model of water we have analyzed the velocity autocorrelation functions to investigate the effect of the liquid milieu on the high-frequency internal modes of molecular motion. The calculations have been made at 1 g ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}3}$ and at 250, 325, and 375 K. Good agreement with experimentally determined pair correlations has also been found.

Aneesur Rahman

Papers

Crystal structure and pair potentials: A molecular-dynamics study

Correlations in the Motion of Atoms in Liquid Argon

Improved simulation of liquid water by molecular dynamics

Molecular Dynamics Study of Liquid Water

Molecular-dynamics study of atomic motions in water