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

Molecular dynamics technique is used to study the homogeneous nucleation of an ordered stable phase from a liquidlike state of aggregation. The rubidium potential is used for a 500 particles system with reduced density 0.95. At the start of the calculation the system is quenched rapidly from a reduced temperature of 0.8 to 0.1. The moment of nucleation and the explosive growth of the nucleus to engulf the whole system have been monitored by studying the characteristics of Voronoi polyhedra in addition to quantities such as temperature, pressure, pair correlation functions, etc. After nucleation, the surface of the nucleus is found to advance at a rate of about 130 m/sec; the size of the critical nucleus is estimated to contain 40 to 70 particles. The ordered stable phase is found to have a bcc structure. In spite of the very rapid rate of cooling which was used to start the calculation, a metastable disordered structure was not obtained.

Crystal nucleation and growth in liquid rubidium

The epitaxial growth of a Lennard-Jones system is studied as a function of substrate temperature ${T}_{s}$ and deposition rate. For all substrate temperatures the growth is into well-ordered layers. Layers become fully completed at intermediate ${T}_{s}$. At very low ${T}_{s}$ the layers contain defects and voids; however, the atoms are still arranged in close-packed islands within the layers.

Role of relaxation in epitaxial growth: A molecular-dynamics study.

We have performed molecular dynamics calculations for a crystalline system in equilibrium to show that by using a fluctuation formula involving the internal stress tensor it is possible to calculate the elastic constants at the ambient temperature with ease and accuracy. The method also allows one to calculate the elastic constants when the system is subjected to an arbitrary external stress.

Molecular dynamics calculation of elastic constants for a crystalline system in equilibrium

A model for the simulation of a solution of an alanine dipeptide in water is presented that combines a previous model for bulk water (ST2) with that used in conformational energy studies on small molecules and proteins. The results of a pilot molecular dynamics study indicate that the model leads to reasonable solvent–solute interactions. No evidence is found for substantial changes in the structure or dynamics of the dipeptide in solution as compared to in vacuo. Furthermore, at the elevated temperature examined, there appear to be no significant effects on the dynamics or intermolecular bonding of the water molecules in contact with the solute.

A model for the simulation of an aqueous dipeptide solution

The motion of ions in Ca2+F2− has been studied by molecular dynamics. The results show that, at 2.525 g cm−3 and 1590 K, the F−’s have a constant of self‐diffusion of 2.6×10−5 cm2 sec−1 and the Ca2+’s form a stable lattice. It is found that half of the F−’s occupy the octahedral sites of the fcc Ca2+ lattice. The details of the self‐diffusion process is analyzed showing the presence of a wave‐vector dependent long relaxation time in the decay of 〈exp(ik⋅u(t) 〉, which is the Fourier transform of the displacement u(t) of the F− ions.

Aneesur Rahman

Papers

Crystal nucleation and growth in liquid rubidium

Role of relaxation in epitaxial growth: A molecular-dynamics study.

Molecular dynamics calculation of elastic constants for a crystalline system in equilibrium

A model for the simulation of an aqueous dipeptide solution

Particle motions in superionic conductors