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    Molecular Dynamics Simulations: Dr.M.Chandra Sekhar

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    Molecular dynamics simulations allow researchers to model molecular systems using computational methods based on classical mechanics or quantum mechanics. They can be used to understand structure and properties of molecules, aid in drug discovery and material research. Simulations provide insights not easily obtainable through experiments alone, such as complete molecular information and testing of theoretical models. Common molecular dynamics packages and force fields are discussed. Radial distribution functions are useful for characterizing spatial structure and molecular distributions in bulk systems.

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    Molecular Dynamics Simulations: Dr.M.Chandra Sekhar

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    Molecular dynamics simulations allow researchers to model molecular systems using computational methods based on classical mechanics or quantum mechanics. They can be used to understand structure and properties of molecules, aid in drug discovery and material research. Simulations provide insights not easily obtainable through experiments alone, such as complete molecular information and testing of theoretical models. Common molecular dynamics packages and force fields are discussed. Radial distribution functions are useful for characterizing spatial structure and molecular distributions in bulk systems.

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    Molecular dynamics simulations allow researchers to model molecular systems using computational methods based on classical mechanics or quantum mechanics. They can be used to understand structure and properties of molecules, aid in drug discovery and material research. Simulations provide insights not easily obtainable through experiments alone, such as complete molecular information and testing of theoretical models. Common molecular dynamics packages and force fields are discussed. Radial distribution functions are useful for characterizing spatial structure and molecular distributions in bulk systems.

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    Download as ppt, pdf, or txt
    28 views24 pages

    Molecular Dynamics Simulations: Dr.M.Chandra Sekhar

    Uploaded by

    chandralove
    Molecular dynamics simulations allow researchers to model molecular systems using computational methods based on classical mechanics or quantum mechanics. They can be used to understand structure and properties of molecules, aid in drug discovery and material research. Simulations provide insights not easily obtainable through experiments alone, such as complete molecular information and testing of theoretical models. Common molecular dynamics packages and force fields are discussed. Radial distribution functions are useful for characterizing spatial structure and molecular distributions in bulk systems.

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    Molecular dynamics Simulations

    Dr.M.Chandra Sekhar
    What is a molecular modeling?
    • Molecular modelling is science, which attains to understand
    the various physical, chemical and biological phenomenon in
    terms of properties of the constituent atoms and molecules.

    • It provides a link between living world of biology and the


    animate world of physics and chemistry

    • Molecular modelling is used to understand and predict the


    structure and properties of atoms and molecules on the basis
    of universal physical laws
    • It finds immense practical use in different
    fields such as Material research, drug
    discovery,
    • The following features of molecular simulations can be
    compared to experiments:
    • As in real experiments, we have to prepare equilibrated samples
    under desired thermodynamic conditions.
    • As in real experiments, we can measure the physical properties
    of the sample.
    • Many different algorithms can reproduce the same physical
    properties within the limit of uncertainties.
    • Because the simulator has access to complete information
    about the state of the model system, there are fewer
    restrictions on which properties can be measured.
    • Accordingly, information and insight can be gleaned from
    simulation that is not only easily obtainable by experiments.
    For example, a comparison of the model’s phase behavior
    can be useful in helping to refine the model parameters.
    • Simulations can be used as test bed for theories.
    What should we learn?
    - the theory behind "molecular modelling"

    - to use program packages designed for molecular electronic


    structure theory

    - to use some molecular visualization packages

    - to do calculations at different levels of theory and to


    interpret the results

    - to make correlations between the experimental and


    theoretical data
    Can we do research?

    • pure theoretical studies

    • coupled experimental and theoretical investigation on


    the structure and properties of molecular systems

    • improving codes for specific physico-chemical


    problems
    Where can we publish the results?
    • Journal of Molecular Structure (Theochem)

    • Journal of Molecular Spectroscopy

    • Chemical Physics

    • Chemical Physics Letters

    • Journal of Molecular Modelling

    • International Journal of Quantum Chemistry

    • Journal of Computational Chemistry

    • Journal of Chemical Physics A

    • The Journal of Chemical Physics

    • Molecular Physics

    • Chemical Reviews

    • Theoretical Chemistry Accounts


    Computational Methods
    There are two main types method depending on the
    starting point theory

    1. Classical method :- Are those method use Newton


    mechanics to model molecular system.

    2. Quantum chemistry method:- Which makes use of


    Quantum mechanics to model the molecular system.
    This method used different type of approximation to
    solve Schrödinger’s Equation.
    Molecular Mechanics
    • Molecular Mechanics is a computational method that

    computes the potential energy surface for a particular

    arrangement of atoms using potential functions that are

    derived using classical physics. These equations are

    known as a force-field
    • Atoms treated as spheres, bonds as springs and
    electron are ignored.

    • It assume that the total potential energy ( Etotal )


    of molecule is given by sum of all the energies
    of attractive and repulsive forces between atom
    in structure.
    The molecular mechanics equation
    • Each molecular mechanics method is characterized by its

    particular force field

    • Force field refers to the functional form and parameter sets

    used to calculate the potential energy of a system of atoms

    in molecular mechanics and molecular dynamics simulations.

    • The parameters of the energy functions may be derived from

    experiments in physics or chemistry, or both.


    Classical empirical force field

    1) AMBER(Assisted Model Building and


    energy Refinement)

    2) CHRAM (Chemistry at Harvard


    Macromolecular Mechanics)

    3) CVFF(Consistent Valence Force Field)


    Molecular dynamics
    • Each atom (i) can be considered as a particle of mass mi and
    charge qi

    • From force Fi and mass mi acceleration of atom at time t can be


    calculated using Newton's second law of motion  Fi  mi .a 
    • From acceleration ,velocity can be calculated.

    • From velocity, position of the atom can be calculated.

    • Hence new position of the atom at time t  t can be calculated.

    • Therefore motion of the atom can be calculated by integrating


    the equation of motion for a given time.
    How MD Simulation is Performed in
    Computer
    • A molecule like (protein, nucleic acids or small molecule) is
    composed of several atoms connected with covalent bonds
    • Each atoms of a molecule is considered as a particle and
    covalent bonds between atoms is considered as springs
    List of molecular dynamics packages

    • Gromacs
    • Amber
    • NAMD
    • MDynaMix
    • Materials Studio
    • LAMMPS
    • DL_POLY
    • CP2K
    • YASARA
    Radial Distribution function
    • Radial distribution functions (RDFs) is the
    fundamental property that characterize the
    averaged spatial structure and the local molecular
    distribution.

    • Radial distribution functions (RDFs) are useful in


    studying intermolecular structure and interactions in
    bulk systems
    • The radial distribution function, (or pair
    correlation function) g(r) in a system
    of particles (atoms, molecules, colloids, etc.),
    describes how density varies as a function of
    distance from a reference particle.

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