MolMod – an open access database of force fields for molecular simulations of fluids

The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de and contains intermolecular force fields for over 150 pure fluids at present. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programmes ms2 and ls1 mardyn, GROMACS, and LAMMPS. To characterise the semantics associated with the numerical database content, a force field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the database were generally optimised such as to yield good representations of experimental data of the vapour–liquid equilibrium with a focus on the vapour pressure and the saturated liquid density. In many cases, the models also yield good predictions of caloric, transport, and interfacial properties of the pure fluids. For all models, references to the original works in which they were developed are provided. The models can be used straightforwardly for predictions of properties of fluid mixtures using established combination rules. Input errors are a major source of errors in simulations. The MolMod database contributes to reducing such errors.     

Molecular dynamics study on perfect and defective graphene/calcium-silicate-hydrate composites under tensile loading

ABSTRACT

Atomic models of graphene/calcium-silicate-hydrate (G/C-S-H) are constructed by embedding perfect or defective graphene in molecular structures of amorphous C-S-H. Molecular dynamics (MD) simulation is utilised to study mechanical properties of the G/C-S-H and the enhancing effect of perfect and defective graphene is compared. The effects of temperature and strain rate on perfect and defective G/C-S-H are also investigated and compared. The results from present simulations show that (i) the defective graphene has better enhancing effect in C-S-H than perfect one and it grows with the increase of defect sizes; (ii) the tensile strength of G/C-S-H decreases with the increase of temperature and the defective G/C-S-H is more susceptible to temperature than the perfect one; (iii) the ultimate strength and the failure strain increase significantly with the increase of strain rate and the effects of strain rate on perfect and defective G/C-S-H are similar. These findings provide important atomic insights for understanding the mechanical behaviours of G/C-S-H composite.     

Strong effect of the interaction potential cut-off on the crystallinity of films grown by simulations

The paper deals with the methodology of film growth simulations using classical molecular dynamics and an empirical interaction potential. We focus on the effect of the cut-off distance (r_C) of the short-range part of the potential. On the one hand, we find that r_C does not affect the qualitative conclusions of the simulations and that its quantitative effect is in the logical direction (better crystallinity at higher r_C). On the other hand, we show that the aforementioned quantitative effect is very strong, and clearly underestimated in the literature. The film crystallinity is affected by (non-)neglecting of as seemingly low energies as several meV per bond. The results are important for the design of growth simulations of crystalline films and for the correct interpretation of their results.     

Molecular dynamics simulation studies of mechanical properties of different carbon nanotube systems

Various mechanical properties of single-walled carbon nanotubes (SWCNT) and double-walled carbon nanotubes (DWCNT) are evaluated using molecular dynamics (MD) simulations. A tensioning process was first performed on a SWCNT whose interaction is based on the Brenner’s ‘second generation’ potential under varying length–diameter ratios and strain rates, in order to understand the SWCNT’s behaviour under axial tension. The results showed an increase in the SWCNT’s ultimate tensile strength and a decrease in critical strain given the conditions of increasing strain rate and a decreasing length–diameter ratio. Comparison was done with previous studies on axial tensioning of SWCNT to validate the results obtained from the set-up, based on the general stress–strain relationship and key mechanical properties such as the strain at failure and the Young’s modulus. A DWCNT was then constructed, and Lennard-Jones ‘12-6’ potential was used to describe the energy present between the nanotube layers. Extraction of the inner tube in a DWCNT was performed using two inner wall tubings of different diameters to draw comparison to the energies needed to separate fully the outer and inner tubing. Finally, a bending test was performed on two DWCNTs with different intertube separations. Insights into the entire bending process were obtained through analyses of the variations in the strain energy characteristic of the surface atoms near the bending site, as the DWCNT is gradually bent until failure.     

Interfacial water on crystalline silica: a comparative molecular dynamics simulation study

Understanding the properties of interfacial water at solid–liquid interfaces is important in a wide range of applications. Molecular dynamics is becoming a widespread tool for this purpose. Unfortunately, however, the results of such studies are known to strongly depend on the selection of force fields. It is, therefore, of interest to assess the extent by which the implemented force fields can affect the predicted properties of interfacial water. Two silica surfaces, with low and high surface hydroxyl density, respectively, were simulated implementing four force fields. These force fields yield different orientation and flexibility of surface hydrogen atoms, and also different interaction potentials with water molecules. The properties for interfacial water were quantified by calculating contact angles, atomic density profiles, surface density distributions, hydrogen bond density profiles and residence times for water near the solid substrates. We found that at low surface density of hydroxyl groups, the force field strongly affects the predicted contact angle, while at high density of hydroxyl groups, water wets all surfaces considered. From a molecular-level point of view, our results show that the position and intensity of peaks observed from oxygen and hydrogen atomic density profiles are quite different when different force fields are implemented, even when the simulated contact angles are similar. Particularly, the surfaces simulated by the CLAYFF force field appear to attract water more strongly than those simulated by the Bródka and Zerda force field. It was found that the surface density distributions for water strongly depend on the orientation of surface hydrogen atoms. In all cases, we found an elevated number of hydrogen bonds formed between interfacial water molecules. The hydrogen bond density profile does not depend strongly on the force field implemented to simulate the substrate, suggesting that interfacial water assumes the necessary orientation to maximise the number of water–water hydrogen bonds irrespectively of surface properties. Conversely, the residence time for water molecules near the interface strongly depends on the force field and on the flexibility of surface hydroxyl groups. Specifically, water molecules reside for longer times at contact with rigid substrates with high density of hydroxyl groups. These results should be considered when comparisons between simulated and experimental data are attempted.     

A molecular dynamics investigation on the compression of cross-linked epoxy resins

Molecular dynamics method is employed to simulate the compression deformation of the polymer materials for electronic packaging. The effects of moisture content, conversion degree, strain rate and temperature on the mechanical properties of epoxy resin are investigated. The stress–strain curves, Young's modulus and Poisson ratio are compared with existing experimental data. The results show that mechanical properties of epoxy resin decrease obviously with increasing moisture content and temperature. However, the high cross-linking conversion and strain rate enhance the mechanical properties of resin.     

On the Atomic Velocities in Molecular and Langevin Dynamics Simulations of Soft-Sphere Systems

Abstract

Time dependent probability distributions of the changes of direction of atomic velocities are considered in order to examine in detail the shape of the trajectories obtained through molecular simulations. We have analysed the atomic motions obtained from molecular dynamics simulations of soft-sphere systems at three very different states, i.e. a dilute fluid, a liquid at high density, and a solid. The methodology has also been used to check the reliability of the velocity evolution obtained when it is assumed that a single particle obeys the generalized Langevin equation and the effect of the other particles is represented by friction and random forces.     

Rff,Conceptual Development of a Full Periodic Table Force Field for Studying Reaction Potential Surfaces

The attributes of a general molecular mechanics force field needed for the study of chemical reactions are described. This attribute set is referred to as a reaction force field (RFF). The functional forms of a first generation reaction force field, RFF1, are presented along with illustrative transition state geometries, activation energies, and reaction coordinate imaginary frequencies. This revised version was published online in June 2006 with corrections to the Cover Date.     

Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads

The end-to-end stretching of a duplex DNA oligonucleotide has been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD) simulations and atomic force microscopy (AFM) experiments. Near quantitative agreement between the calculations and experiments was obtained for both the extension length and forces associated with strand separation. The PMF calculations show that the oligonucleotide extends without a significant energetic barrier from a length shorter than A-DNA to a length 2.4 times the contour length of B-DNA at which the barrier to strand separation is encountered. Calculated forces associated with the barrier are 0.09±0.03 nN, based on assumptions concerning tip and thermal-activated barrier crossing contributions to the forces. Direct AFM measurements show the oligonucleotide strands separating at 2.6±0.8 contour lengths with a force of 0.13±0.05 nN. Analysis of the energies from the MD simulations during extension reveals compensation between increases in the DNA-self energy and decreases in the DNA-solvent interaction energy, allowing for the barrierless extension of DNA beyond the canonical B form. The barrier to strand separation occurs when unfavorable DNA interstrand repulsion cannot be compensated for by favorable DNA-solvent interactions. The present combination of single molecule theoretical and experimental approaches produces a comprehensive picture of the free energy surface of biological macromolecular structural transitions. Received: 2 June 1998 / Revised version: 25 January 1999 / Accepted: 11 February 1999     

An Efficient,Box Shape Independent Non-Bonded Force and Virial Algorithm for Molecular Dynamics

Abstract

A notation is introduced and used to transform a conventional specification of the non-bonded force and virial algorithm in the case of periodic boundary conditions into an alternative specification. The implementation of the transformed specification is simpler and typically a factor of 1.5 faster than a conventional implementation. Moreover, it is generic with respect to the shape of the simulated system, i.e. the same routines can be used to handle triclinic boxes, truncated octahedron boxes etc. An implementation of this method is presented, and the speed achieved on various machines is given. Essence of the new method is that the number of calculations of image particle positions is strongly reduced during non-bonded force calculations.