scholarly journals Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Wolfgang Schreiner ◽  
Rudolf Karch ◽  
Bernhard Knapp ◽  
Nevena Ilieva
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Time Intervals ◽  
Variable Time ◽  
Dynamics Simulations ◽  
Stationary Shape

Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.

Molecular dynamics simulations of nanoscale and sub-nanoscale friction behavior between graphene and a silicon tip: analysis of tip apex motion

Nanoscale ◽  
2015 ◽  
Vol 7 (14) ◽  
pp. 6295-6303 ◽  
Author(s):  
Hong Min Yoon ◽  
Youngmo Jung ◽  
Seong Chan Jun ◽  
Sasidhar Kondaraju ◽  
Joon Sang Lee
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Simulation System ◽  
Friction Behavior ◽  
Simulation Process ◽  
Nanoscale Friction ◽  
Detailed Simulation ◽  
Dynamics Simulations

Schematic of (a) MD simulation system, (b) detailed simulation process, and (c) FFM experiment setup.

The folding mechanism and key metastable state identification of the PrP127–147 monomer studied by molecular dynamics simulations and Markov state model analysis

2017 ◽  
Vol 19 (18) ◽  
pp. 11249-11259 ◽  
Author(s):  
Shuangyan Zhou ◽  
Qianqian Wang ◽  
Yuwei Wang ◽  
Xiaojun Yao ◽  
Wei Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Structural Dynamics ◽  
Md Simulation ◽  
Markov State Model ◽  
Markov State ◽  
Folding Mechanism ◽  
State Identification ◽  
Dynamics Simulations

MD simulation combined with MSM analysis was employed to investigate the structural dynamics and the folding mechanism of the key fragment 127–147 monomer of prion protein.

scholarly journals Variable time domain discretization methodology for molecular dynamics simulation of metallic compounds

2021 ◽  
Author(s):  
Jamal Zeinalov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Time Step ◽  
Variable Time ◽  
Metallic Compounds ◽  
Dynamics Simulations ◽  
Computational Resources

The present work proposes a methodology to improve the computational requirements of molecular dynamics simulations while maintaining or improving the fidelity of the obtained results. The most common method of molecular dynamics simulation at present is the multi-force, constant time-step, explicit computation, which advances a single time step at a time to determine the next state of the system. The present work proposes a variable time-step strategy, where a single large simulation is subdivided into multiple time domains which redistribute computational resources where they are needed the most: in areas of higher than average potential or kinetic energy or highly dynamic areas around impurity clusters, void formations and crack propagations. The research focuses on the simulation of metallic compounds, as these form the basis of most common molecular dynamics simulations, and have been very thoroughly investigated over the years, thus providing a very extensive body of work for the purpose of comparison and validation of the proposed methodology. The novel methodology presented in this work allows to alleviate some of the limitations associated with the molecular dynamics methodologies and go beyond traditional scales of simulation. The proposed method has been observed to deliver 5 to 20 percent increase in simulation size domain while maintaining or improving the accuracy and computational cycle time. The benefits were observed to be greater for large simulations with one or more areas of higher than average kinetic or potential energy levels, such as those found during crack initiation and propagation, coating-substrate interface, localized pressure application or large thermal gradient. The large difference allows for very clear prioritization of computational resources for high energy areas and as a result provides for faster and more accurate simulation even with increased domain size. Conversely, this method has been observed to provide little to no benefit when simulating stable systems that are undergoing very slow change, such as (relatively) slow change in ambient temperature or pressure, or otherwise homogeneous internal and external boundary conditions. However, for the majority of applications described above, including coating deposition and additive manufacturing, the proposed methodology will yield substantial increase in both simulation size and accuracy, since in the aforementioned processes kinetic and potential energy gradients across the simulation are typically very significant

Dipropargyl ether bisphenol A based boron-containing polymer: synthesis, characterization and molecular dynamics simulations of the resulting pyrolysis and carbonization

RSC Advances ◽  
2015 ◽  
Vol 5 (5) ◽  
pp. 3390-3398 ◽  
Author(s):  
N. Gao ◽  
X. Jiang ◽  
Y. H. Liu
Keyword(s):  
Molecular Dynamics ◽  
Bisphenol A ◽  
Molecular Dynamics Simulations ◽  
Time Evolution ◽  
Small Molecule ◽  
Md Simulation ◽  
Polymer Synthesis ◽  
Color Code ◽  
Pyrolysis Products ◽  
Dynamics Simulations

The time evolution of major pyrolysis products including small-molecule species of a dipropargyl ether bisphenol A based novel boron-containing polymer was examined via ReaxFF-MD simulation (Color code: C, grey; O, red; H, white; B, yellow).

Mechanical Properties of Vacancy-containing Graphene and Graphite Estimated by Molecular Dynamics Simulations

2011 ◽  
Vol 1362 ◽  
Author(s):  
Akihiko Ito ◽  
Shingo Okamoto
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Tensile Strength ◽  
Molecular Dynamics Simulations ◽  
Young’S Modulus ◽  
Md Simulation ◽  
Pristine Graphene ◽  
Cluster Type ◽  
Slip Deformation ◽  
Dynamics Simulations

ABSTRACTUsing molecular dynamics (MD) simulation, we investigated the mechanical properties of graphene and graphite, which contain cluster-type vacancies. We found that as the vacancy size increases, the tensile strength drastically decreases to at least 56% of that of pristine graphene, whereas Young’s modulus hardly changes. In vacancy-containing graphene, we also found that slip deformation followed by fracture occurs under zigzag tension. In general, tensile strength decreases as the size of cluster-type vacancies increases. However, the tensile strength of graphene with a clustered sextuple vacancy increases as the vacancy disappears because slip deformation proceeds. Furthermore, we found that slip deformation by vacancies in graphite occurs less easily than in graphene.Our results suggest that the shape of vacancies affects the strengths of graphene and graphite.

Seawater desalination using pillared graphene as a novel nano-membrane in reverse osmosis process: nonequilibrium MD simulation study

2018 ◽  
Vol 20 (34) ◽  
pp. 22241-22248 ◽  
Author(s):  
Sayyed Jalil Mahdizadeh ◽  
Elaheh K. Goharshadi ◽  
Golnoosh Akhlamadi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Reverse Osmosis ◽  
Simulation Study ◽  
Md Simulation ◽  
Nonequilibrium Molecular Dynamics ◽  
Seawater Desalination ◽  
Dynamics Simulations ◽  
Graphene Nanostructures

Herein, the applicability and efficiency of two types of pillared graphene nanostructures, namely, (6,6)@G and (7,7)@G, were investigated as membranes in reverse osmosis seawater desalination using extensive nonequilibrium molecular dynamics simulations.

Molecular Dynamics Simulations and the Landauer’s Principle

2018 ◽  
Vol 25 (02) ◽  
pp. 1850006
Author(s):  
Ihab H. Naeim ◽  
J. Batle ◽  
S. Kadry ◽  
O. Tarawneh
Keyword(s):  
Molecular Dynamics ◽  
Information Theory ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Canonical Ensemble ◽  
Md Simulations ◽  
Present Contribution ◽  
Bistable Potential ◽  
Landauer’S Principle ◽  
Dynamics Simulations

Landauer’s principle is a fundamental link between thermodynamics and information theory, which implies that the erasure of information comes at an energetic price. In the present contribution we analyze to what extend the usual molecular dynamics (MD) simulation formalism can handle the Landauer’s bound kBT ln 2 in the simplest case of one particle treated classically. The erasure of one bit of information is performed by adiabatically varying the shape of a bistable potential in a full cycle. We will highlight the inadequacy of either the microcanonical or canonical ensemble treatments currently employed in MD simulations and propose potential solutions.

Adsorption behavior of Cs+ ions to vermiculite demonstrated by molecular dynamics simulations

2018 ◽  
Vol 28 (01n02) ◽  
pp. 1-5
Author(s):  
Akira Takeuchi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Constant Pressure ◽  
Md Simulations ◽  
Kinetic Process ◽  
Adsorption Behavior ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Cs Ions

The present paper discusses the simulation results, performed by classical molecular dynamics (MD), for vermiculite. The kinetic process of the [Formula: see text] ions in water that are adsorbed into vermiculite [Formula: see text] was investigated with classical MD simulations utilizing Coulomb and Born–Mayer–Huggins potentials. A monoclinic vermiculite crystal with a [Formula: see text] supercell was placed into 8461 molecules of water to form a rectangular supercell of [Formula: see text]. The water was placed into contact with both sides of the [Formula: see text]–[Formula: see text] planes of the vermiculite crystal, along the [Formula: see text]-axis only. The rectangular supercells, which were prepared with the vermiculite in water with and without an additional 200 [Formula: see text] ions, were simulated. The MD conditions included a constant pressure ensemble for 1 ps at a constant step of 0.1 fs. The results revealed an increase in the distances of the [Formula: see text] layers at the interface between the vermiculite and water. This increase in the separation of the [Formula: see text] layers was suitable for the uptake of [Formula: see text] ions by the vermiculite. The accelerated MD simulation which replaced the interfacial [Formula: see text] ions with [Formula: see text] ions tended to include the [Formula: see text] ions into the vermiculite by excluding the [Formula: see text] ions.

scholarly journals Variable time domain discretization methodology for molecular dynamics simulation of metallic compounds

2021 ◽  
Author(s):  
Jamal Zeinalov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Time Step ◽  
Variable Time ◽  
Metallic Compounds ◽  
Dynamics Simulations ◽  
Computational Resources

The present work proposes a methodology to improve the computational requirements of molecular dynamics simulations while maintaining or improving the fidelity of the obtained results. The most common method of molecular dynamics simulation at present is the multi-force, constant time-step, explicit computation, which advances a single time step at a time to determine the next state of the system. The present work proposes a variable time-step strategy, where a single large simulation is subdivided into multiple time domains which redistribute computational resources where they are needed the most: in areas of higher than average potential or kinetic energy or highly dynamic areas around impurity clusters, void formations and crack propagations. The research focuses on the simulation of metallic compounds, as these form the basis of most common molecular dynamics simulations, and have been very thoroughly investigated over the years, thus providing a very extensive body of work for the purpose of comparison and validation of the proposed methodology. The novel methodology presented in this work allows to alleviate some of the limitations associated with the molecular dynamics methodologies and go beyond traditional scales of simulation. The proposed method has been observed to deliver 5 to 20 percent increase in simulation size domain while maintaining or improving the accuracy and computational cycle time. The benefits were observed to be greater for large simulations with one or more areas of higher than average kinetic or potential energy levels, such as those found during crack initiation and propagation, coating-substrate interface, localized pressure application or large thermal gradient. The large difference allows for very clear prioritization of computational resources for high energy areas and as a result provides for faster and more accurate simulation even with increased domain size. Conversely, this method has been observed to provide little to no benefit when simulating stable systems that are undergoing very slow change, such as (relatively) slow change in ambient temperature or pressure, or otherwise homogeneous internal and external boundary conditions. However, for the majority of applications described above, including coating deposition and additive manufacturing, the proposed methodology will yield substantial increase in both simulation size and accuracy, since in the aforementioned processes kinetic and potential energy gradients across the simulation are typically very significant

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