Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. The accumulated influence of these fluctuations is crucial ...

We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental ...

Hydrogen desorption from hydride matrix is still an open field of research. By means of accurate first-principle molecular dynamics (MD) simulations an Mg–MgH2 interface is selected, studied and characterized. Electronic structure calculations are used to determine the equilibrium properties and the behavior of the surfaces in terms of structural deformations and total energy considerations. Fu...

The work on molten salts and isotope separation performed over the years at Université Pierre et Marie Curie and at Collège de France is critically reviewed. This research, closely related to A. Klemm’s pioneering contributions, leads among other things to the discovery of the effect now called the ‘Chemla effect’, after the late Professor Marius Chemla. These studies of ionic motions in melts,...

Parallel Molecular Dynamics Stencil has been developed to execute effectively large-scale parallel molecular dynamics simulations. The Stencil is adapted to varieties of molecular dynamics simulations without special attention to parallelization techniques. As an example of large-scale simulation using this Stencil, the adiabatic elastic constants of solid argon in crystalline and amorphous sta...

The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical an...

A quantum-mechanically-based potential energy function that describes interactions of dimers of the explosive cyclotrimethylenetrinitramine (RDX) is used to predict polymorphic structures of crystalline RDX. The potential was first used in crystal structure prediction methods which generate polymorphs of RDX and provide a 0 K ordering in energy. The 13 low energy-structures generated by crystal...

An integrated computational method which couples classical molecular dynamics simulations with density functional theory calculations is used to simulate the solid-state NMR spectra of amorphous CaSiO(3). Two CaSiO(3) glass models are obtained by shell-model molecular dynamics simulations, successively relaxed at the GGA-PBE level of theory. The calculation of the NMR parameters (chemical shiel...

Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields, which have been developed and validated using relatively short simulations of small molecules, become apparent. One common artifact is aggregation of water-soluble b...

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide ...