Welcome to the Molecular Dynamics 101 repository! This repository contains lessons and things I learned during the course of my PhD in the field of Molecular Dynamics. The topics covered range from fundamental concepts to important algorithms used to propagate systems. This repository will serve as an example repository for future MD online courses that I'll generate.
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🧪 'forcefield_parameterization': This folder contains tutorials on parameterizing GAFF forcefield using semi-empirical quantum chemistry methods and Hartree-Fock RESP charges obtained from Gaussian with the Merz-Kollman scheme. Link
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🔬 'fundamental_eqs': This folder contains examples of fundamental equations employed in standard molecular dynamics simulations, such as LJ interactions, harmonic interactions, etc. A Python script shows the simulation of LJ interactions; harmonic potential scripts will be added soon. Link
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⚙️ 'openmm_md': This folder contains instructions on how to run typical MD simulations using the OpenMM MD package. An example of 'ibrutinib' is used to demonstrate the working. A Python script is included to show the full-stack production run from minimization to output in an NVT ensemble. Link
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🌐 'qmmm_optimization': This folder provides a tutorial on performing hybrid QM/MM geometry optimization using the Amber-Gaussian interface. Link
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⏲️ 'thermostat': This folder includes a Python script demonstrating the working of Langevin dynamics using Argon atoms. Link
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🧪🔬 'amber_md': Running Amber MD simulations using the AmberTools package: Input scripts on running either simple molecular dynamics or a full-on production level molecular dynamics simulations. Link
Feel free to explore each subfolder for detailed explanations, code examples, and tutorials!