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Molecular Simulations of Biomolecules
This introductory seminar will provide an overview of the most commonly used computational tools for studying biomolecules, mainly focusing on potential energy function and its evaluation, general molecular dynamic simulation algorithm, and current methods for free energy calculations implemented in molecular simulation package GROMACS. From the early use of computers to study various aspects of liquids and gases by modeling them as hard spheres, computer simulations now days are routinely used to study dynamics of complex molecules such as proteins, carbohydrates, nucleic acids, and lipid membranes.
Computer simulations have became a useful tool in understanding the dynamics and mechanism of function of these molecules with atomistic details. New sampling methods coupled with increased computational resources have made it possible to simulate the folding of small peptides and proteins. The underlying parameters or force-fields used in atomistic representation have matured to the point that free energies calculated using computer simulations methods are in quantitative agreements with experiments.