Visual Molecular Dynamics

Résumé

Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. History VMD has been developed under the aegis of principal investigator Klaus Schulten in the Theoretical and Computational Biophysics group at the Beckman Institute for Adv

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https://en.wikipedia.org/wiki/Visual_Molecular_Dynamics

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Introduction to molecular dynamics and Monte-Carlo simulation methods.

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Impurities are known to have a significant impact on materials properties. In particular, the presence of impurities can change mechanical properties and stabilize the microstructure by reducing grain growth and recrystallization processes. In the past atomistic simulations, in particular molecular dynamics, have contributed a lot to the understanding of deformation mechanisms in nanocrystalline metals. Especially, insights into details of dislocation/GB interactions have been gained. Additionally, simulations on coupled grain boundary migration in bicrystalline samples have played an important role in understanding stress assisted grain growth in nanocrystalline metals. However, all these simulations have been performed on monatomic systems. This means that the role of impurities has not yet been considered in these simulations. Some of the important difference between experiments and simulations could be removed by introducing dilute O distributions to computational Al samples. For this purpose, a simulation method is required which can deal with the oxidation of Al atoms around the O impurities and which can simulate the ionic and metallic nature of bonding simultaneously. Here, a method is suggested which fulfills the requirements by modifying the variable charge method of Streitz and Mintmire [Phys. Rev. B 50, 11996 (1994)]. A local chemical potential approach which optimizes the charge on only those atoms expected to be ionic is developed. Additionally the EAM potential for the non-electrostatic interaction given in the publication of Streitz and Mintmire is substituted by empirical potentials which treat the Al-Al interactions with a well-known Al potential. The Al-O and O-O interactions in these EAM potentials are fitted for the simulation of dilute O impurities in Al and additionally for the simulation of corundum in case of a second potential. The aforementioned developments are applied to study the effect of O impurities on the deformation of nc Al. A fully three-dimensional nc sample containing 15 grains of 12 nm grain-size is deformed with a dilute O content in the triple junction lines. The impact of O impurities on dislocation propagation is also considered in a sample which consists of a single grain extracted from a large molecular dynamics simulation. This simulation geometry contains a perfect dislocation, which is pinned at the surrounding grain boundary network. Therefore it allows the study of pinning strength and after unpinning the propagation behavior of the dislocation under various O impurity distributions. Additionally, the role of O impurities on coupled GB migration is investigated by studying two bicrystalline samples with different O distributions in both of them. In the discussion, the emphasis is on the simulation method. Especially, the significance of the samples, simulation conditions and the performance of the method in the different applications are discussed. Additionally, the different developments (local chemical potential approach and EAM potentials) are critically analyzed and improvements for future simulations of impurities are suggested.

EPFL2010

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H-aggregates featuring tight π-stacks of the conjugated heterocyclic cores represent ideal morphologies for 1D organic semiconductors. Such nanofibrils have larger electronic couplings between the adjacent cores compared to the herringbone crystal or amorphous assemblies. In this work, we show that for a set of seven structurally and electronically distinct cores, including quaterthiophene and oligothienothiophenes, the co-planar dimer model captures the impact of the monomer’s electronic structure on charge transport, but more advanced multiscale modelling, featuring molecular dynamics and kinetic Monte-Carlo simulations, is needed to account for the packing and disorder effects. The differences in the results between these two computational approaches arise from the sensitivity of the electronic coupling strength to the relative alignment of adjacent cores, in particular the long-axis shift between them, imposed by the oligopeptide side chains. Our results demonstrate the dependence of the performance of H-aggregates on the chemical nature of the cores and the presence of the side chains, as well as the limitations in using the simple dimer model for a rapid computational pre-screening of the conjugated cores.

Royal Soc Chemistry2017

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Charge transport in AgI subject to an external magnetic field is studied via computer simulations. We demonstrate that a recently developed algorithm can effectively complement problematic experiments to detect the ionic Hall effect, and identify previously unreported effects such as ionic magnetoresistance. We focus first on the charge transport properties of superionic AgI, showing that the magnetic field induces a considerable reduction in the diagonal elements of the conductivity tensor (magnetoresistance). Within the limits of the signal-to-noise ratio, calculation of the off-diagonal elements of this tensor also shows the onset of the Hall effect in this material. We then present numerical evidence supporting the use of the Nerst-Einstein approximation to obtain the Hall mobility of the system. This approximation enables very efficient detection of the Hall signal, with values of the mobility and of the migration activation energy in very good agreement with experiments. Having validated our simulation approach, we consider melted AgI to investigate if the Hall signal persists in this nonsuperionic case, finding a detectable signal. Comparison of the diffusion tensor of this system with that of molten NaCl also indicates why the Hall signal is absent in the latter. This work paves the way for the routine use of simulations to study transport, and in particular the ionic Hall effect, in ionic systems under external magnetic field.

Amer Physical Soc2016

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EPFL2010