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MD Simulation

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MD Simulation

A molecular dynamics simulation is a potential function, or a description of the terms by which the particles in the simulation will interact. In chemistry and biology this is usually known as a force field and in materials physics as an interatomic potential. Potentials may be defined at many levels of physical accuracy; those most commonly used in chemistry are based on molecular mechanics and embody a classical mechanics treatment of particle-particle interactions that can reproduce structural and conformational changes but usually cannot reproduce chemical reactions.

In classical molecular dynamics, the effect of the electrons is approximated as one potential energy surface, usually showing the ground state.

MD can be performed using certain program packages to simulate protein flexibility. All of the programs are free for academic users. The first MD package, Amber (Assisted Model Building with Energy Refinement), was originally developed for refining NMR structures. The name ‘Amber’ refers to both force fields for the simulation of biomolecules and the MD program package. The most widely used force field versions are Amber94, Amber99SB, and Amber03. The next one, CHARMM (Chemistry at HARvard Macromolecular Mechanics), also known for both force fields and the program package. It was originally developed by Martin Karplus of Harvard University, USA. It is the oldest biomolecular MD package. CHARMM-GUI provides a web-based graphical tool for setting up input files for the simulation. GROMACS (GROningen MAchine for Chemical Simulations) typically runs 3–10 times faster than other MD programs. Unlike Amber and CHARMM, GROMACS does not have its own force field. Instead, it can import Amber, CHARMM, GROMOS, and the OPLS force field to run MD simulation. The unique feature of the program is that it is open-source software released under the GPL license. NAMD (NAnoscale Molecular Dynamics) is developed by the Theoretical and Computational Biophysics Group at the University of Illinois, Urbana-Champaign, USA. It is designed to efficiently run on parallel machines for simulating large molecules. The program has high compatibility with other MD programs such as CHARMM, since NAMD has the same input, output, and force field formats as CHARMM.


Molecular dynamics simulation is a computational method that calculates the time dependent behavior of a molecular system.  MD simulations have provided detailed information on the fluctuations and conformational changes of proteins and nucleic acids.   These methods are now routinely used to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes. They are also used in the determination of structures from x-ray crystallography and from NMR experiments.

Applications

  • Predict how every atom in a protein or other molecular system will move over time, based on a general model of the physics governing interatomic interactions. 
  • These simulations can capture a wide variety of important biomolecular processes, including conformational change, ligand binding, and protein folding, revealing the positions of all the atoms at femtosecond temporal resolution. 
  • Predict how biomolecules will respond at an atomic level to perturbations such as mutation, phosphorylation, protonation, or the addition or removal of a ligand. 

MD simulations are often used in combination with a wide variety of experimental structural biology techniques, including x-ray crystallography, cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET)

Tools

  • Abalone (molecular mechanics)
  • AMBER
  • CHARMM
  • GROMACS
  • GROMOS
  • SHARC molecular dynamics software
  • MacroModel
  • MDynaMix

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