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Molecular dynamics
About: Molecular dynamics is a research topic. Over the lifetime, 22482 publications have been published within this topic receiving 800625 citations. The topic is also known as: molecular dynamics.
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TL;DR: The parmbsc0 force field as mentioned in this paper is a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the a/g concerted rotation in nucleic acids (NAs).
1,982 citations
TL;DR: In this article, the authors review the applications of free energy calculations employing molecular dynamics or Monte Carlo methods to a variety of chemical and biochemical phenomena, including molecular solvation, molecular association, macromolecular stability, and enzyme catalysis.
Abstract: The author will review the applications of free energy calculations employing molecular dynamics or Monte Carlo methods to a variety of chemical and biochemical phenomena. The focus is on the applications of such calculations to molecular solvation, molecular association, macromolecular stability, and enzyme catalysis. The molecules discussed range from monovalent ions and small molecules to proteins and nucleic acids.
1,960 citations
TL;DR: Several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers, and some capabilities recently added to the code which were enabled by this flexibility are highlighted.
1,956 citations
TL;DR: An extensive study of 59 ligands interacting with six different proteins finds that MM/PBSA can serve as a powerful tool in drug design, where correct ranking of inhibitors is often emphasized, and the accuracy of the binding free energies calculated by three Generalized Born (GB) models is evaluated.
Abstract: The Molecular Mechanics/Poisson−Boltzmann Surface Area (MM/PBSA) and the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free energies for macromolecules by combining molecular mechanics calculations and continuum solvation models. To systematically evaluate the performance of these methods, we report here an extensive study of 59 ligands interacting with six different proteins. First, we explored the effects of the length of the molecular dynamics (MD) simulation, ranging from 400 to 4800 ps, and the solute dielectric constant (1, 2, or 4) on the binding free energies predicted by MM/PBSA. The following three important conclusions could be observed: (1) MD simulation length has an obvious impact on the predictions, and longer MD simulation is not always necessary to achieve better predictions. (2) The predictions are quite sensitive to the solute dielectric constant, and this parameter should be carefully determined according to the characteristics of the protein/lig...
1,926 citations
TL;DR: A class of interatomic potential models that can be automatically generated from data consisting of the energies and forces experienced by atoms, as derived from quantum mechanical calculations, are introduced.
Abstract: We introduce a class of interatomic potential models that can be automatically generated from data consisting of the energies and forces experienced by atoms, as derived from quantum mechanical calculations. The models do not have a fixed functional form and hence are capable of modeling complex potential energy landscapes. They are systematically improvable with more data. We apply the method to bulk crystals, and test it by calculating properties at high temperatures. Using the interatomic potential to generate the long molecular dynamics trajectories required for such calculations saves orders of magnitude in computational cost.
1,923 citations