RESOURCES

Molecular Simulations help to comprehend many biological processes from the dangling motions of biomolecules. Are you keen to enter this fantasy world and not sure where to start? The books and the links listed here will provide you the basic understanding…

Books

• Andrew R. Leach, Molecular Modelling: Principles and Applications, 2nd Edition, 2001, Prentice Hall

• Tamar Schlick, Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd Edition, 2010, Springer

• Mark E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, 2010, Oxford Univ. Press

• Daan Frenkel, Berend Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd Edition, 2002 Academic Press.

• Michael Feig (Editor), Modeling Solvent Environments: Applications to Simulations of Biomolecules, 2010, Wiley-VCH Verlag GmbH.

• Gregory A. Voth (Editor), Coarse-Graining of Condensed Phase and Biomolecular Systems, 2009, CRC Press.

Links

• Tool to visualize biomolecule: http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html

• Tutorial to run MD using GROMACS http://www.mdtutorials.com/gmx/

• GROMACS Manual https://ftp.gromacs.org/pub/manual/manual-5.0.4.pdf

• Tutorial to run MD using NAMD http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html

• Martini coarse grained simulation tutorial http://cgmartini.nl/index.php/tutorials

• Plugins to analyze MD trajectory https://www.plumed.org/

• Python code to read, write and analyze MD trajectory https://mdtraj.org/1.9.4/index.html

• Molecular Docking using AutoVina Dock http://vina.scripps.edu/

• Python Tutorial https://docs.python.org/3/tutorial/

• C++ Tutorial http://www.cplusplus.com/doc/tutorial/