SUMMARY Computer simulations are giving way to more complex and accurate studies of biological membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories comprises the biophysical characterization of membrane properties or the study of protein-lipid interactions and dynamics. However, there is a lack of automated tools to analyse MD simulations of complex membrane or memb...

The development in the 1950s and 1960s of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quan...

In this paper, we propose coarse-grained single-site (CGSS), wall-CO(2), and CO(2)-CO(2) interaction potential models to study the structure of carbon dioxide under confinement. The CGSS potentials are used in an empirical potential based quasi-continuum theory, EQT, to compute the center-of-mass density and potential profiles of CO(2) confined inside different size graphite slit pores. Results...

Molecular dynamics (MD) simulations have been used to study surface reaction dynamics of Si and Si02 etching by halogens. To perform classical MD simulations for Si02 etching reaction by halogens (C1 or F), we have constructed new sets of twoand three-body interatomic potential functions based on potential energy data obtained from ab initio quantum mechanical calculations of the electronic sta...

Molecular dynamics (MD) is a field of study in computational chemistry concerned with describing and simulating the motion of atoms and molecules in time. Such simulations give information about time-dependent physical and chemical processes as well as provide statistical information such as diffusion coefficients, heat capacities, or time-correlation functions for a chemical system of interest...

Molecular dynamics (MD) simulations play an increasingly important role in many aspects of biochemical research but are often not part of the biochemistry curricula at the undergraduate level. This article discusses the pedagogical value of exposing students to MD simulations and provides information to help instructors consider what software and hardware resources are necessary to successfully...

In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed. Some software sets such as GROMACS are used for that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. This paper describes many improvemen...

The data described here supports the research article "Unraveling HIV Protease Flaps Dynamics by Constant pH Molecular Dynamics Simulations" (Soares et al., 2016) [1]. The data involves both standard Molecular Dynamics (MD) and Constant pH Molecular Dynamics (CpHMD) to elucidate the effect of protonation states of catalytic dyad on the HIV-PR conformation. The data obtained from MD simulation d...

Crystal structures of acetylcholinesterase complexed with ligands are compared with side-chain conformations accessed by native acetylcholinesterase in molecular dynamics (MD) simulations. Several crystallographic conformations of a key residue in a specific binding site are accessed in a simulation of native acetylcholinesterase, although not seen in rotomer plots. Conformational changes upon ...

Molecular Dynamics (MD) simulation and Density Functional Theory (DFT) methods have been used to evaluate the efficiency of four quinoline derivatives on corrosion inhibition in the aqueous phase. Some quantum chemical parameters such as hardness (η), electrophilicity (w), polarizability (a), energy of the highest occupied molecular orbital (EHOMO), energy of th...