Dive into the second session of a Gromacs beginner tutorial on Molecular Dynamics Simulations. Learn essential MD simulation steps, including system solvation, neutralization, energy minimization, and equilibration. Explore how to generate and interpret RMSD and RMSF graphs in Windows. Access provided .mdp files for ions, minimization, NVT, NPT, and MD simulations to enhance your practical understanding. Follow along with step-by-step instructions on using mdrun, analyzing potential energy, and performing equilibration with grompp. Gain valuable insights into bioinformatics and computational chemistry techniques for studying molecular systems.
Molecular Dynamics Simulations with Gromacs - Beginner Tutorial Session 2
Bioinformatics With BB via YouTube
Overview
Syllabus
Intro
Add solvent system
Neutralize system
Energy minimization
mdrun
potential energy
equilibrate system
growmpp
NVT
Pressure
Steps
Analysis
Taught by
Bioinformatics With BB
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