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Molecular Dynamics

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Master molecular dynamics simulations using GROMACS, path integral methods, and force field analysis to model complex biomolecular systems. Learn through hands-on tutorials on YouTube and advanced courses on edX, covering everything from basic protein simulations to DNA macromolecule dynamics and conformational transitions.

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Bioinformatics With BB
Molecular Dynamics Simulation with GROMACS - Installation and Beginner Tutorial
3 reviews

Step-by-step guide to install GROMACS and run a beginner-level molecular dynamics simulation of a protein in water, covering both Windows and Linux platforms.
- YouTube
- 24 minutes
- On-Demand
- Free Video
Bioinformatics With BB
Molecular Dynamics Simulations with Gromacs - Beginner Tutorial Session 2

Learn MD simulation steps, RMSD/RMSF graph generation in Windows using Gromacs. Covers system preparation, energy minimization, equilibration, and analysis for molecular dynamics simulations.
- YouTube
- 24 minutes
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NPTEL-NOC IITM
Basic Introduction to Molecular Dynamics

Explore molecular dynamics fundamentals, LAMMPS usage, visualization techniques, and key concepts like interatomic potentials and periodic boundary conditions.
- YouTube
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Valence Labs
Timewarp: Transferable Acceleration of Molecular Dynamics by Time-Coarsened Dynamics

Explore Timewarp: a transferable method for accelerating molecular dynamics simulations using normalizing flows, enhancing sampling efficiency for equilibrium properties of molecular systems.
- YouTube
- 55 minutes
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- Free Video
Valence Labs
Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics

Explore accelerated molecular dynamics simulation using Timewarp, a transferable AI method for efficient sampling of molecular systems and discovery of metastable states.
- YouTube
- 1 hour 15 minutes
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Valence Labs
Path Integral Stochastic Optimal Control for Sampling Transition Paths in Molecular Dynamics

Explore stochastic optimal control for sampling molecular transition paths, considering full geometry without relying on collective variables. Applicable to larger proteins like Polyproline and Chignolin.
- YouTube
- 1 hour 7 minutes
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Erwin Schrödinger International Institute for Mathematics and Physics (ESI)
A Coarse-Grained Molecular Dynamics Study of Damage Localization During the Fracture of Double Polymer Networks

Explore molecular dynamics of damage localization in double polymer networks, focusing on mechanisms behind increased toughness and the interplay between load sharing and damage propagation.
- YouTube
- 14 minutes
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ICTP-SAIFR
Quantifying Large-Scale Dynamics of Complex Molecular Assemblies

Explore quantitative methods for analyzing large-scale dynamics in complex molecular systems, focusing on advanced techniques and their applications in molecular biophysics.
- YouTube
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Materials Cloud
Car-Parrinello Molecular Dynamics - Parallelization Part 1

Discover Car-Parrinello molecular dynamics and parallelization techniques for computational materials science simulations.
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Materials Cloud
Car-Parrinello Molecular Dynamics - Adiabaticity, Metals, Thermostats and Barostats - 06

Explore Car-Parrinello molecular dynamics covering adiabaticity, metals, thermostats, barostats, and correlation times in computational materials science.
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Materials Cloud
Molecular Dynamics - Thermostats, Barostats and Nuclear Quantum Effects - 16

Explore advanced molecular dynamics techniques including thermostats, barostats, and nuclear quantum effects in computational materials science simulations.
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- 1 hour 18 minutes
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- Free Video
Institute for Pure & Applied Mathematics (IPAM)
Molecular Dynamics of Solutions out of Equilibrium

Explore advanced molecular dynamics simulation methods for electrochemical systems and crystal growth in non-equilibrium solutions with novel computational approaches.
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- 42 minutes
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- Free Video
Institute for Pure & Applied Mathematics (IPAM)
Molecular Dynamics Simulation for Electrochemical Systems - Challenges of Field Fluctuation

Explore molecular dynamics simulations for electrochemical systems, focusing on electric field applications, VASP implementation, and machine learning force fields for electrostatic interactions.
- YouTube
- 45 minutes
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- Free Video
Bogolyubov Institute for Theoretical Physics
Using ChatGPT in Molecular Dynamics Simulations - Applications to Nucleic Acids

Discover how to leverage ChatGPT for molecular dynamics simulations, focusing on nucleic acids analysis and computational physics applications in DNA research.
- YouTube
- 1 hour 1 minute
- On-Demand
- Free Video
Bogolyubov Institute for Theoretical Physics
Force Fields and Molecular Dynamics Simulations - Applications to Nucleic Acids

Dive into molecular dynamics simulations and force fields, exploring their practical applications in nucleic acid research through advanced computational physics methods and theoretical frameworks.
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