A Quantitative Assessment of the Potential of Implicit Integration Methods for Molecular Dynamics Simulation

2010 ◽  
Vol 5 (3) ◽  
Author(s):  
Nick Schafer ◽  
Dan Negrut
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Time Integration ◽  
Dynamics Simulation ◽  
Integration Step ◽  
Implicit Integration ◽  
Implicit Methods ◽  
Current Standard ◽  
Step Size ◽  
Computational Overhead

Implicit integration, unencumbered by numerical stability constraints, is attractive in molecular dynamics (MD) simulation due to its presumed ability to advance the simulation at large step sizes. It is not clear what step size values can be expected and if the larger step sizes will compensate for the computational overhead associated with an implicit integration method. The goal of this paper is to answer these questions and thereby assess quantitatively the potential of implicit integration in MD. Two implicit methods (midpoint and Hilber–Hughes–Taylor) are compared with the current standard for MD time integration (explicit velocity Verlet). The implicit algorithms were implemented in a research grade MD code, which used a first-principles interaction potential for biological molecules. The nonlinear systems of equations arising from the use of implicit methods were solved in a quasi-Newton framework. Aspects related to a Newton–Krylov type method are also briefly discussed. Although the energy conservation provided by the implicit methods was good, the integration step size lengths were limited by loss of convergence in the Newton iteration. Moreover, a spectral analysis of the dynamic response indicated that high frequencies present in the velocity and acceleration signals prevent a substantial increase in integration step size lengths. The overhead associated with implicit integration prevents this class of methods from having a decisive impact in MD simulation, a conclusion supported by a series of quantitative analyses summarized in the paper.

Implicit Integration in Molecular Dynamics Simulation

2008 ◽  
Author(s):  
Nicholas P. Schafer ◽  
Radu Serban ◽  
Dan Negrut
Keyword(s):  
Molecular Dynamics ◽  
Newton Method ◽  
Dynamics Simulation ◽  
Integration Scheme ◽  
Implicit Integration ◽  
Step Size ◽  
Time Step ◽  
Integration Methods ◽  
Size Limitation ◽  
Quasi Newton

Molecular Dynamics (MD) simulation is a versatile methodology that has found many applications in materials science, chemistry and biology. In biology, the models employed range from mixed quantum mechanical and fully atomistic to united atom and continuum mechanical. These systems are evolved in discrete time by solving Newton’s equations of motion at each time step. The numerical methods currently in use limit the step size of a typical all atom simulation to 1 femtosecond. This step size limitation means that many steps need to be taken in order to reach biologically relevant time scales. At each time step, an evaluation of the forces on each atom must be performed resulting in heavy computational loads. This work investigates the use of implicit integration methods in MD. Implicit integration methods have been proven superior to their explicit counterparts in classical mechanical simulation, with which MD has many similarities. Longer time steps reduce the number of force evaluations that must be performed and the corresponding computational load. Herein we present results that compare implicit integration techniques with the current standard for molecular dynamics, the explicit velocity Verlet integration scheme. Total energy conservation is used as a metric for evaluating the dependability of simulations in the microcanonical ensemble. In order to understand the nature of the problem, several long simulations were run and analyzed by performing a Fourier analysis on the position, velocity and acceleration signals. Lastly, several methods for improving the viability of implicit integration methods are considered including replacing the Jacobian used in the Quasi-Newton method with a constant, diagonal mass matrix, evaluating the Jacobian infrequently and finding a better prediction of the system configuration to improve the convergence of the Quasi-Newton method.

scholarly journals Molecular dynamics simulation of sI methane hydrate under compression and tension

2020 ◽  
Vol 18 (1) ◽  
pp. 69-76
Author(s):  
Qiang Wang ◽  
Qizhong Tang ◽  
Sen Tian
Keyword(s):  
Molecular Dynamics ◽  
Methane Hydrate ◽  
Fracture Process ◽  
Md Simulation ◽  
Maximum Stress ◽  
Dynamics Simulation ◽  
Tensile Fracture ◽  
Maximum Compressive Stress ◽  
Motion State ◽  
Stress States

AbstractMolecular dynamics (MD) analysis of methane hydrate is important for the application of methane hydrate technology. This study investigated the microstructure changes of sI methane hydrate and the laws of stress–strain evolution under the condition of compression and tension by using MD simulation. This study further explored the mechanical property and stability of sI methane hydrate under different stress states. Results showed that tensile and compressive failures produced an obvious size effect under a certain condition. At low temperature and high pressure, most of the clathrate hydrate maintained a stable structure in the tensile fracture process, during which only a small amount of unstable methane broke the structure, thereby, presenting a free-motion state. The methane hydrate cracked when the system reached the maximum stress in the loading process, in which the maximum compressive stress is larger than the tensile stress under the same experimental condition. This study provides a basis for understanding the microscopic stress characteristics of methane hydrate.

Molecular Dynamics Simulation of AFM-Based Nanomachining Processes

2011 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan ◽  
Ashlie Martini
Keyword(s):  
Molecular Dynamics ◽  
Friction Coefficient ◽  
Md Simulation ◽  
Computational Models ◽  
Dynamics Simulation ◽  
Radius Of Curvature ◽  
Force Microscopy ◽  
Indentation Force ◽  
Atomic Force ◽  
Development And Validation

Recently, atomic force microscopy (AFM) has been widely used for nanomachining and fabrication of micro/ nanodevices. This paper describes the development and validation of computational models for AFM-based nanomachining (nanoindentation and nanoscratching). The Molecular Dynamics (MD) technique is used to model and simulate mechanical indentation and scratching at the nanoscale in the case of gold and silicon. The simulation allows for the prediction of indentation forces and the friction force at the interface between an indenter and a substrate. The effects of tip curvature and speed on indentation force and friction coefficient are investigated. The material deformation and indentation geometry are extracted based on the final locations of atoms, which are displaced by the rigid tool. In addition to modeling, an AFM was used to conduct actual indentation at the nanoscale, and provide measurements to validate the predictions from the MD simulation. The AFM provides resolution on nanometer (lateral) and angstrom (vertical) scales. A three-sided pyramid indenter (with a radius of curvature ∼ 50 nm) is raster scanned on top of the surface and in contact with it. It can be observed from the MD simulation results that the indentation force increases as the depth of indentation increases, but decreases as the scratching speed increases. On the other hand, the friction coefficient is found to be independent of scratching speed.

Molecular dynamics simulation of homogeneous nucleation of supersaturated potassium chloride (KCl) in aqueous solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (48) ◽  
pp. 7507-7518 ◽  
Author(s):  
Soroush Ahmadi ◽  
Yuanyi Wu ◽  
Sohrab Rohani
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Potassium Chloride ◽  
Homogeneous Nucleation ◽  
Md Simulation ◽  
Crystal Nucleation ◽  
Dynamics Simulation

Molecular dynamics (MD) simulation is used to investigate the mechanism of crystal nucleation of potassium chloride (KCl) in a supersaturated aqueous solution at 293 K and 1 atm.

scholarly journals Material Analysis and Molecular Dynamics Simulation for Cavitation Erosion and Corrosion Suppression in Water Hydraulic Valves

Materials ◽  
2020 ◽  
Vol 13 (2) ◽  
pp. 453 ◽  
Author(s):  
Masoud Kamoleka Mlela ◽  
He Xu ◽  
Feng Sun ◽  
Haihang Wang ◽  
Gabriel Donald Madenge
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Essential Role ◽  
Corrosion Inhibitors ◽  
Cavitation Erosion ◽  
Dynamics Simulation ◽  
Preference Ranking ◽  
Water Hydraulics ◽  
The Impact ◽  
Hydraulic Valves

In the milestone of straggling to make water hydraulics more advantageous, the choice of coating polymer for water hydraulics valves plays an essential role in alleviating the impact of cavitation erosion and corrosion, and this is a critical task for designers. Fulfilling the appropriate selection, we conflicted properties that are vital for erosion and corrosion inhibitors, as well as the tribology in the sense of coefficient of friction. This article aimed to choose the best alternative polymer for coating on the selected substrate, that is, Cr2O3, Al2O3, Ti2O3. By applying PROMETHEE (Preference Ranking Organization Method for Enrichment Evaluations), the best polymer obtained with an analyzed performance attribute is Polytetrafluoroethylene (PTFE) that comes up with higher outranking (0.5932052). A Molecular Dynamics (MD) simulation was conducted to identify the stronger bonding with the regards of the better cleave plane between Polytetrafluoroethylene (PTFE) and the selected substrate. Polytetrafluoroethylene (PTFE)/Al2O3 cleaved in (010) plane was observed to be the strongest bond in terms of binding energy (3188 kJ/mol) suitable for further studies.

scholarly journals Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond

2020 ◽  
Vol 21 (7) ◽  
pp. 2512
Author(s):  
Lu-Lu Yin ◽  
Jia-Kun Xu ◽  
Xiao-Juan Wang ◽  
Shu-Qin Gao ◽  
Ying-Wu Lin
Keyword(s):  
Molecular Dynamics ◽  
Disulfide Bond ◽  
Rational Design ◽  
Double Mutant ◽  
Md Simulation ◽  
Experimental Studies ◽  
Heme Iron ◽  
Dynamics Simulation ◽  
Fluoride Ion ◽  
Artificial Proteins

Protein design is able to create artificial proteins with advanced functions, and computer simulation plays a key role in guiding the rational design. In the absence of structural evidence for cytoglobin (Cgb) with an intramolecular disulfide bond, we recently designed a de novo disulfide bond in myoglobin (Mb) based on structural alignment (i.e., V21C/V66C Mb double mutant). To provide deep insight into the regulation role of the Cys21-Cys66 disulfide bond, we herein perform molecular dynamics (MD) simulation of the fluoride–protein complex by using a fluoride ion as a probe, which reveals detailed interactions of the fluoride ion in the heme distal pocket, involving both the distal His64 and water molecules. Moreover, we determined the kinetic parameters of fluoride binding to the double mutant. The results agree with the MD simulation and show that the formation of the Cys21-Cys66 disulfide bond facilitates both fluoride binding to and dissociating from the heme iron. Therefore, the combination of theoretical and experimental studies provides valuable information for understanding the structure and function of heme proteins, as regulated by a disulfide bond. This study is thus able to guide the rational design of artificial proteins with tunable functions in the future.

Newmark-Beta Method in Discrete Elastic Rods Algorithm to Avoid Energy Dissipation

2019 ◽  
Vol 86 (8) ◽  
Author(s):  
Weicheng Huang ◽  
Mohammad Khalid Jawed
Keyword(s):  
Energy Dissipation ◽  
Time Integration ◽  
Integration Scheme ◽  
Integration Step ◽  
Elastic Rods ◽  
Computationally Efficient ◽  
Step Size ◽  
Time Step ◽  
Time Step Size ◽  
Time Integration Scheme

Discrete elastic rods (DER) algorithm presents a computationally efficient means of simulating the geometrically nonlinear dynamics of elastic rods. However, it can suffer from artificial energy loss during the time integration step. Our approach extends the existing DER technique by using a different time integration scheme—we consider a second-order, implicit Newmark-beta method to avoid energy dissipation. This treatment shows better convergence with time step size, specially when the damping forces are negligible and the structure undergoes vibratory motion. Two demonstrations—a cantilever beam and a helical rod hanging under gravity—are used to show the effectiveness of the modified discrete elastic rods simulator.

scholarly journals Preparation and Molecular Dynamics Simulation of RDX/MUF Nanocomposite Energetic Microspheres with Reduced Sensitivity

Processes ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 692
Author(s):  
Jia ◽  
Hu ◽  
Xu ◽  
Liu ◽  
Ma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Emulsion Polymerization ◽  
Md Simulation ◽  
Urea Formaldehyde ◽  
Urea Formaldehyde Resin ◽  
Experimental Results ◽  
Dynamics Simulation ◽  
Formaldehyde Resin ◽  
Process Conditions

In order to improve the general problem of irregular coating morphology and low mechanical strength of the coating layer in existing coating desensitization technology, nano-cyclotrimethylene trinitramine/melamine-urea-formaldehyde (RDX/MUF) composite energetic microspheres were prepared by an improved emulsion polymerization, taking the MUF as the binder and RDX as the main explosive. In order to judge whether RDX/MUF possessed good stability, the combination of differential scanning calorimetry (DSC) and molecular dynamics (MD) simulation was used to determine the level of binding binding energy between urea-formaldehyde resin binder (UF) and RDX. In addition, to investigate the optimal reaction temperature for the preparation of MUF/RDX, the binding energy between UF and RDX at different temperatures was simulated. And then the morphology and thermal properties of the as-prepared composite energetic microspheres were analyzed by scanning electron microscopy (SEM) and DSC, the impact sensitivity and friction sensitivity of the resultant samples were tested as well. Moreover, RDX/MUF with the same MUF content was prepared by physical mixing for comparative analysis. MD simulation demonstrated that UF and RDX possessed good binding ability at 298 K. The DSC method indicatec that UF and RDX had good compatibility, and the comprehensive performance of RDX after coating was not significantly deteriorated; The optimal binding temperature between UF and RDX was 60~70 °C which is consistent with the experimental results. The experimental results showed that the optimum process conditions for the preparation of RDX/MUF could be listed as follows: the temperature for preparing RDX/MUF composite energetic microspheres by the improved emulsion polymerization was 70 °C the optimal pH value of the urea-formaldehyde resin prepolymer solution was 3, and the optimal melamine-urea molar ratio was 0.4.

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