Results 21 to 30 of about 621,380 (345)
Replica-exchange molecular dynamics simulation for supercooled liquids [PDF]
, 2000 We investigate to what extend the replica-exchange Monte Carlo method is able to equilibrate a simple liquid in its supercooled state. We find that this method does indeed allow to generate accurately the canonical distribution function even at low ...
Kob, Walter, Yamamoto, Ryoichi
core +2 more sources
Virtual-Wall Model for Molecular Dynamics Simulation
Molecules, 2016 A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time.
Lijuan Qian +3 more
doaj +1 more source
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
BMC Bioinformatics, 2023 Background The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue
Ivo Henrique Provensi Vieira +5 more
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Molecular dynamics simulations of biomolecules [PDF]
Nature Structural Biology, 2002 Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function ...
Martin Karplus, J. Andrew McCammon
openaire +6 more sources
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
eLife, 2022 Spike (S) protein is the primary antigenic target for neutralization and vaccine development for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It decorates the virus surface and undergoes large motions of its receptor binding domains (
Hisham M Dokainish +5 more
doaj +1 more source
Molecular dynamics simulation of uranium nitride oxidation [PDF]
Journal of the Serbian Chemical SocietyA molecular dynamic simulation of the uranium mononitride (UN) oxidation in an Ar–O medium in the temperature range of 373–2073 K is performed. The study is performed for UN particles with a crystalline and amorphous structure at an oxygen concentration ...
Galashev Alexander Y. +4 more
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Computational and Structural Biotechnology Journal, 2023 We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations.
Angelo Felline +4 more
doaj +1 more source
Molecular mode-coupling theory for supercooled liquids: Application to water
, 1999 We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition.
A. Latz +26 more
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Molecular Dynamics Simulation of Coherent Interfaces in Fluorite Heterostructures [PDF]
, 2014 The standard model of enhanced ionic conductivities in solid electrolyte heterostructures follows from a continuum mean-field description of defect distributions that makes no reference to crystalline structure.
Madden, Paul A., Morgan, Benjamin J.
core +3 more sources
Molecular Dynamics Simulation of Sympathetic Crystallization of Molecular Ions
, 2003 It is shown that the translational degrees of freedom of a large variety of molecules, from light diatomic to heavy organic ones, can be cooled sympathetically and brought to rest (crystallized) in a linear Paul trap.
A. Fioretti +31 more
core +1 more source