Transcript
INTRODUCTION TO MOLECULAR DYNAMICS
SIMULATION
By,Shreeman, C.S
Division of BioinformaticsFaculty of life sciences
Jagadguru Sri Shivarathreeswara UniversityMysuru- 570015
Simulation - computer simulation
Molecular dynamics - definition - quantum mechanics - statistical mechanics
Schrodinger equation
Introduction
H^ ψ=Eψ
approaches to solve the problems
Force field
Methods and steps to integrate the equation
Methodological changes
Applications - protein folding : structure prediction - GPCR
Some classical MD package - AMBER - CHARMM - Gromacs - Tinker
Molecular dynamics: survey of methods for simulating the activity of proteins.
By Adcock SA1, McCammon JA chem. Rev. 2006
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics
Ben Cooke1 and Scott C. Schmidler. J. Chem.. phys. 2008,129
Simulating water with rigid non-polarizable models: a general perspective
Carlos Vega, Jose LF Abascal. Phy.chem.2001.
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