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.