Computational and Theoretical Chemistry
                Molecular Dynamics Simulations

Linux :

• SSH for Windows: Download
• The Linux command line for beginner
• Basic Linux Commands for Beginners


Computational Chemistry (reading) :

Classical molecular dynamics simulations
• Classical Molecular Dynamics by from NIC series, 2002
• Introduction to Molecular Dynamics Simulationby from NIC series, 2004
• Force fields and molecular dynamics simulations, 2011
• Computer Simulation of Liquids [Ch. 1, 2, 3, 5 and 6]

Ab initio/First principles molecular dynamics simulations
• Ab initio molecular dynamics: Theory and
• Ab initio molecular dynamics: Concepts, recent developments, and future trends



• Essentials of Computational Chemistry [Ch. 1 - 10 ]
• Understanding Molecular Simulation
• First principles simulations
• First principles MD: link
  

Computational Chemistry (NPTEL video courses) :

• Computational methods and programming [ Weeks 1, 2, 11, and 12 for MSc project students]
• Computational chemistry and Classical molecular dynamics with programming [ Weeks 6, 7 and 8]
• Statistical mechanics
• Classical thermodynamics

Molecular Dynamics Packages

• Introduction to Molecular Dynamics [Link to video]
• Molecular Dynamics 5 mins [Link to video]
• Gromacs Instllation and test [Link]
• Gromacs - Running Simulations mostly default mode [Link]
• Gromacs - One more how to [Link]
• Introduction to LAMMPS - Molecular Dynamics package [Link to video]
• LAMMPS Workshop 2019 [Link to video]

Computational chemistry Calculations
• General - 1 | 2
• DFT methods, Basis set, Transition State - 1 | 2 | 3 | 4 | 5
• TS Calc - 1 | 2
• S_N2 reactions and TS - 1
• CompOrg - 1
• VASP [Link to video]

Visualization packages
• VESTA - 1 | 2 | 3 | 4 | 5 | 6 |
• Grace - Introduction
• Grace - Curve fitting

Some teaching tools
• Goodnotes | LiveBoard | Piazza | Quizizz | googleclassroom

Teaching Quantum Mechanics with MATLAB

• Carleton College - Northfield, MN
• Applied Quantum Mechanics, 2e

• 1 |



Writing workshops:


• Manuscript formatting
• How to write a research Paper
• Research Paper Calculator
• Dissertation Calculator


Journals: Scopus probable journals


• Journal of Chemical Theory and Computation [5.3]
• The Journal of Physical Chemistry A
• The Journal of Physical Chemistry B
• The Journal of Physical Chemistry C
• J. of Chemical Information and Modeling[3.8]
• Chemistry of Material
• ACS Appl. Energy Mater.
• ACS Sustainable Chem. Eng.
• The Journal of Chemical Physics
• Journal of Molecular Liquids[4.5]
• Chemical Physics
• Chemical Physics Letter
• Computational and Theoretical Chemistry[1.4]
• ChemPhysChem[2.9]
• J. Computational Chemistry[3.2]
• Theoretical Chemistry Accounts[1.5]
• Molecular Physics
• Journal of Molecular Modeling




Misc:


• Mypianonotes application
• Online tools