Michael L. Klein

Comparison of simple potential functions for simulating liquid water

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.

Nosé–Hoover chains: The canonical ensemble via continuous dynamics

Nose has derived a set of dynamical equations that can be shown to give canonically distributed positions and momenta provided the phase space average can be taken into the trajectory average, i.e., the system is ergodic [S. Nose, J. Chem. Phys. 81, 511 (1984), W. G. Hoover, Phys. Rev. A 31, 1695 (1985)]. Unfortunately, the Nose–Hoover dynamics is not ergodic for small or stiff systems. Here a modification of the dynamics is proposed which includes not a single thermostat variable but a chain of variables, Nose–Hoover chains. The ‘‘new’’ dynamics gives the canonical distribution where the simple formalism fails. In addition, the new method is easier to use than an extension [D. Kusnezov, A. Bulgac, and W. Bauer, Ann. Phys. 204, 155 (1990)] which also gives the canonical distribution for stiff cases.

Constant pressure molecular dynamics for molecular systems

Technical aspects of the constant pressure molecular dynamics (MD) method proposed by Andersen and extended by Parrinello and Rahman to allow changes in the shape of the MD cell are discussed. The new MD method is extended to treat molecular systems and to include long range charge-charge interactions. Results on the conservation laws, the frequency of oscillation of the MD cell, and the equations which constrain the shape of the MD cell are also given. An additional constraint is introduced to stop the superfluous MD cell rotation which would otherwise complicate the analysis of crystal structures. The method is illustrated by examining the behaviour of solid nitrogen at high pressure.

Explicit reversible integrators for extended systems dynamics

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 compared with the standard implicit (iterative) integrators on some illustrative example problems. In addition, modification of the proposed algorithms for multiple time step integration is outlined.

A polarizable model for water using distributed charge sites

An algorithm is proposed for treating many‐body polarization effects that is suitable for molecular dynamics simulations of polar fluids. As an application of the procedure we have augmented an existing point charge model for water. Using reasonable parameters, the characteristic water structure and liquid binding energy can be reproduced. The resulting effective dipole moment of a water molecule in water is found to be 2.85 D.

Intermolecular potential functions and the properties of water

Abstract A wide range of gas, liquid and solid state properties are calculated using most of the presently available potential functions for the water pair interaction. It is shown that no one model gives a satisfactory account of all three phases. We propose a new semi-empirical model that has some success as an effective pair potential in all three phases.

Coarse grain models and the computer simulation of soft materials

This article presents a topical review of coarse grain simulation techniques. First, we motivate these techniques with illustrative examples from biology and materials science. Next, approaches in the literature for increasing the efficiency of atomistic simulations are mentioned. Considerations related to a specific coarse grain modelling approach are discussed at length, and the consequences arising from the loss of detail are given. Finally, a large number of results are presented to give the reader a feeling for the types of problem which can be addressed.

Large-scale molecular dynamics simulations of self-assembling systems.

Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

A new implementation of the adaptive biasing force (ABF) method is described. This implementation supports a wide range of collective variables and can be applied to the computation of multidimensional energy profiles. It is provided to the community as part of a code that implements several analogous methods, including metadynamics. ABF and metadynamics have not previously been tested side by side on identical systems. Here, numerical tests are carried out on processes including conformational changes in model peptides and translocation of a halide ion across a lipid membrane through a peptide nanotube. On the basis of these examples, we discuss similarities and differences between the ABF and metadynamics schemes. Both approaches provide enhanced sampling and free energy profiles in quantitative agreement with each other in different applications. The method of choice depends on the dimension of the reaction coordinate space, the height of the barriers, and the relaxation times of degrees of freedom in the orthogonal space, which are not explicitly described by the chosen collective variables.

Pairwise additive effective potentials for nitrogen

A number of pairwise additive intermolecular potentials have been used in the study of properties of nitrogen in the solid, liquid and gas phases. It is shown that a simple model can account satisfactorily for a wide range of phenomena.