Volume 21, Issue 2 , May and June 2014, , Pages 362-369
Abstract
Background: Molecular dynamics method to simulate the thermodynamic behavior of materials in the solid phase, liquid and gas using the force, velocity and position of particles. Among these factors, the most important factor is power. Classical molecular dynamics simulations, Classical potential energy ...
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Background: Molecular dynamics method to simulate the thermodynamic behavior of materials in the solid phase, liquid and gas using the force, velocity and position of particles. Among these factors, the most important factor is power. Classical molecular dynamics simulations, Classical potential energy is obtained. potential classic, is a function of the location and position of electrons in atoms or nuclei of atoms is dependent. purpose of this study compare the energy calculated for a number of biologically important proteins.
Materials and Methods: Molecular dynamics simulation provide an appropriate way to microscopic atomic and molecular modeling. The calculations were performed on a personal computer with the program hyperchem. No changes were made and geometry of all atoms, Dihedral angles and bonds were self-change.
Results: The final energy of protein structures using Monte-Carlo simulations, molecular dynamics and Langevin dynamics was performed. Optimize the geometry and the interaction energies calculated with different methods, for several proteins, including nerve growth factor receptor and enzyme protein was comparable effective learning.
Conclusion: Molecular dynamics simulations of quantum and classical potential energy of the electron Schrödinger equation is calculated. Simulation methods using a set of non-equilibrium transport properties and consider the effects of quantum mechanics are developed. Energy potential and the degree during the heat simulations almost constant that indicates the stability of the temperature structure of these proteins are listed.