Multibody Molecular Dynamics I: Theoretical Development

2007 ◽  
Author(s):  
Rudranarayan M. Mukherjee ◽  
Kurt S. Anderson
Keyword(s):  
Molecular Dynamics ◽  
Multibody Dynamics ◽  
Temporal Integration ◽  
Interaction Force ◽  
Theoretical Development ◽  
Coarse Grained ◽  
Unified Framework ◽  
Multi Scale ◽  
Integration Schemes ◽  
Dynamics Simulations

This is the first paper in a series of two papers on using multibody dynamics algorithms and methods for coarse-grained molecular dynamics simulations. This paper presents the underlying framework for multi-scale modelling of biomolecules and polymers. In this framework, the system to be simulated is sub-structured into a hierarchy of multi-resolution models that are simulated using efficient multibody dynamics algorithms. The algorithms work in a unified framework, enabling efficient multi-scale (or multi-resolution) simulations. A discussion of the hierarchy of models with different resolutions along with the salient features of the appropriate multibody dynamics algorithms used for simulating them is presented. The unified scheme and the qualitative advantages of the method are discussed. Important implementation details such as boundary conditions, temporal integration schemes, interaction force field calculations and solvent models are also presented. In the next paper applications and results are discussed.

scholarly journals An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guy G. Butcher ◽  
William S. Harwin ◽  
Chris I. Jones
Keyword(s):  
Molecular Dynamics ◽  
Alpha Helix ◽  
Interaction Force ◽  
Coiled Coils ◽  
Coarse Grained ◽  
Simulation Framework ◽  
Force Estimation ◽  
Model And Simulation ◽  
Target Force ◽  
Dynamics Simulations

AbstractThe alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb’s law shows a simulated force interaction within the physiological relevant range of 5–40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2–3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.

Multibody Molecular Dynamics II: Applications and Results

2007 ◽  
Author(s):  
Rudranarayan M. Mukherjee ◽  
Paul Crozier ◽  
Kurt S. Anderson
Keyword(s):  
Molecular Dynamics ◽  
Multibody Dynamics ◽  
Degrees Of Freedom ◽  
Coarse Grained ◽  
Future Research ◽  
Conservation Of Energy ◽  
Order Of Magnitude ◽  
Speed Up ◽  
The Stability ◽  
Dynamics Simulations

This is the second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include water boxes, alkane chains, alanine dipeptide and carboxyl terminal fragments of Calmodulin, Ribosomal, and Rhodopsin proteins. The atomistic representations of these systems include several thousand degrees of freedom and results of several nano-second simulations of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.

scholarly journals The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models

2021 ◽  
Vol 12 ◽  
Author(s):  
Dashuai Lv ◽  
Jingyuan Li ◽  
Sheng Ye
Keyword(s):  
Molecular Dynamics ◽  
Bound States ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Multi Scale ◽  
Switch Mechanism ◽  
Dynamics Simulations ◽  
Cooperative Assembly ◽  
Computational Strategy

Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformational dynamics of assembled FtsZ. We found that the top end of a filament is highly dynamic and can undergo T-to-R transitions in both GTP- and GDP-bound states. We observed several subcategories of nucleation related dimer species, which leading to a feasible nucleation pathway. In addition, we observed that FtsZ filament exhibits noticeable amounts of twisting, indicating a substantial helicity of the FtsZ filament. These results agree with the previously models and experimental data. Anisotropy network model (ANM) analysis revealed a polymerization enhanced assembly cooperativity, and indicated that the cooperative motions in FtsZ are encoded in the structure. Taken together, our study provides a molecular-level understanding of the diversity of the structural states of FtsZ and the relationships among polymerization, hydrolysis, and cooperative assembly, which should shed new light on the molecular basis of FtsZ’s cooperativity.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

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