Subsections
[Cr:4, Lc:3, Tt:0, Lb:1]
- Foundations of Molecular mechanics and Classical description of molecules.
- Potential Energy surfaces and optimization methods.
- Potentials for bonded and non-bonded interactions: classical and polarizable forcefields.
- Tackling electrostatics and long-range interactions.
- Monte carlo simulations.
- Statistical mechanics application to macroscopic ensembles.
- Algorithms to integrate equations of motion with use of thermostats and barostats.
- Measuring thermodynamic, structural and dynamical properties of equilibrium systems: transport coefficients; space-dependent and time-dependent correlation coefficients.
- Advanced practices of MD:
- Coarse-grained models for molecule description.
- Free energy calculations: alchemical transformation, Thermodynamic Integration methods.
- Enhanced sampling techniques: Umbrella sampling, Steered MD, Targeted MD, replica.
- exchange sampling.
- Metadynamics and Adaptive biasing forces (ABF).
- Extending to QM-MM hybrid simulation and first principle ab-initio simulation.
- Familiarity with basic LINUX commands.
- Setting up and running conventional MD simulation with different ensembles and barostats.
- Analysis of trajectories.
- Setting up and running free energy calculations via perturbation methods.
- Analyzing the FEP results.
- Setting up and running enhanced MD simulations eg Steered MD, umbrella sampling, ABF simulations.
- Setting up and running small QM-MM and Ab-initio simulations.
- MD Softwares: NAMD, CPMD, AMBER, CHARMM, MMTSB.
- Visualization Softwares: VMD, Pymol.
- lotting Softwares: Gnuplot, R.
- M. P. Allen and D. J. Tildesley, Computer Simulations of Liquids, Oxford Clarendon Press (1989).
- A. R. Leach, Molecular Modelling, Principles and Applications, 2nd edition, Pearson Education Ltd. UK (2001).
- D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd edition, Academic Press UK (2001).
- D. C. Rapaport, The Art of Molecular Dynamics Simulations, 2nd edition,Cambridge University UK (2004).
- T. Schlick, Molecular Modeling and Simulations. An Interdisciplinary Guide, 2nd edition, Springer Verlag, New York (2010).
