DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package

Smith, William R.; Forester, Timothy R.

doi:10.1016/s0263-7855(96)00043-4

Cited by 2,155 publications

(1,578 citation statements)

References 23 publications

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“…All the simulations described in this paper were performed with classical molecular dynamics in the DL POLY 3.09 20 code. Periodic boundary conditions were applied in all three dimensions with an ACC slab effectively separated from its periodic image by a slab of water in the Z-direction.…”

Section: Methodsmentioning

confidence: 99%

How does an amorphous surface influence molecular binding? – ovocleidin-17 and amorphous calcium carbonate

Freeman

Harding

Quigley

et al. 2015

Phys. Chem. Chem. Phys.

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Atomistic molecular dynamics simulations of dehydrated amorphous calcium carbonate interacting with the protein Ovocleidin-17 are presented. These simulations demonstrate that the amorphisation of the calcium carbonate surface removes water structure from the surface. This reduction of structure allows the protein to bind with many residues, unlike on crystalline surfaces where binding is strongest when only a few residues are attached to the surface. Basic residues are observed to dominate the binding interactions. The implications for protein control over crystallisation are discussed.

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Section: Methodsmentioning

confidence: 99%

How does an amorphous surface influence molecular binding? – ovocleidin-17 and amorphous calcium carbonate

Freeman

Harding

Quigley

et al. 2015

Phys. Chem. Chem. Phys.

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“…All molecular dynamics simulations were performed using the DL_POLY 2 [47] code applying the Verlet Leap Frog algorithm with a timestep of 0.2 fs for shell masses of 0.2 amu. For equilibration the NPT (variable volume) ensemble was used whereas production was carried out within the NVT (constant volume) ensemble by applying Nose-Hoover thermostats and Hoover barostats with relaxation times of 0.5 ps as appropriate.…”

Section: Methodsmentioning

confidence: 99%

Growth modification of seeded calcite using carboxylic acids: Atomistic simulations

Aschauer

Spagnoli

Bowen

et al. 2010

Journal of Colloid and Interface Science

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a b s t r a c tMolecular dynamics simulations were used to investigate possible explanations for experimentally observed differences in the growth modification of calcite particles by two organic additives, polyacrylic acid (PAA) and polyaspartic acid (p-ASP). The more rigid backbone of p-ASP was found to inhibit the formation of stable complexes with counter-ions in solution, resulting in a higher availability of p-ASP compared to PAA for surface adsorption. Furthermore the presence of nitrogen on the p-ASP backbone yields favorable electrostatic interactions with the surface, resulting in negative adsorption energies, in an upright (brush conformation). This leads to a more rapid binding and longer residence times at calcite surfaces compared to PAA, which adsorbed in a flat (pancake) configuration with positive adsorption energies. The PAA adsorption occurring despite this positive energy difference can be attributed to the disruption of the ordered water layer seen in the simulations and hence a significant entropic contribution to the adsorption free energy. These findings help explain the stronger inhibiting effect on calcite growth observed by p-ASP compared to PAA and can be used as guidelines in the design of additives leading to even more marked growth modifying effects.

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“…[43][44][45] The simulations have been performed using the DL_POLY program. 46 The temperature and pressure of the systems have been kept constant by means of the weak coupling algorithms of Berendsen et al 47 Equations of motion have been integrated using the leap-frog algorithm, with an integration time step of 0.2 fs. Systems have been equilibrated for 5 ns.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

The local environment of the molecules in water–DMSO mixtures, as seen from computer simulations and Voronoi polyhedra analysis

Idriss

Marekha

Киселев

et al. 2015

Phys. Chem. Chem. Phys.

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Running title: Voronoi analysis of water-DMSO mixtures * Electronic mail: nacer.idrissi@univ-lille1.fr (A.I), pali@chem.elte.hu (P. J.) 2 Graphical and textual abstract for the contents page:The local structure of DMSO-water mixtures is studied by computer simulation and Voronoi analysis 3 AbstractMolecular dynamics simulations of water- DMSO mixtures, containing 10,20,30,40,50, 60, 70, 80, and 90 mol% DMSO, respectively, have been performed on the isothermalisobaric (N,p,T) ensemble at T = 298 K and at the pressure equal to the experimental vapor pressure at each mixture composition. In addition, simulations of the two neat systems have also been performed for reference. The potential models used in the simulations are known to excellently reproduce the mixing properties of these compounds. The simulation results have been analyzed in detail by means of the Voronoi polyhedra (VP) of the molecules.Distributions of the VP volume and asphericity parameter as well as that of the radius of the spherical intermolecular voids have been calculated. Detailed analyses of these distributions have revealed that both molecules prefer to be in an environment consisting of both types of molecules, but the affinity of DMSO for mixing with water is clearly stronger than that of water for mixing with DMSO. As a consequence, the dilution of the two neat liquids by the other component has been found to follow different mechanisms: when DMSO is added to neat water small domains of neat-like water persist up to the equimolar composition, whereas no such domains are found when neat DMSO is diluted by water. The observed behavior is also in line with the fact that the main thermodynamic driving force behind the full miscibility of water and DMSO is the energy change accompanying their mixing, and that the entropy change accompanying this mixing is negative in systems of low, and positive in systems of high DMSO mole fractions. Finally, we have found a direct evidence for the existence of strong hydrogen bonded complexes formed by one DMSO and two water molecules, but it has also been shown that these complexes are in equilibrium with single (monomeric) water and DMSO molecules in the mixed systems.4

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DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package

Cited by 2,155 publications

References 23 publications

How does an amorphous surface influence molecular binding? – ovocleidin-17 and amorphous calcium carbonate

How does an amorphous surface influence molecular binding? – ovocleidin-17 and amorphous calcium carbonate

Growth modification of seeded calcite using carboxylic acids: Atomistic simulations

The local environment of the molecules in water–DMSO mixtures, as seen from computer simulations and Voronoi polyhedra analysis

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