Machine Learning for Molecular Dynamics

Welcome to Machine Learning for Molecular Dynamics - BMB 961 Sec 003

Course Materials

Syllabus
Course Schedule
Software Setup Guide
Final Project Description

Week 01

Week 01 Lecture: Welcome to ML4MD
Week 01 Lab: Python Refresher Course
LearnPython.zip
BMB_Community_Standards.pdf
sEH_nowater.pdb
sEH_unbinding.dcd

Week 02

Week 02 Lecture: Machine Learning at the Intersection with Molecular Simulations
Week 02 Lab: Machine Learning Basics
apple.vacuum.dat
apple.vacuum.highres.dat
apple.leaf.air.highres.dat

Week 03

Week 03 Lecture: Neural Network Architectures
Week 03 Lab: Convolutional Networks
aq15_pdbs.tgz
aq15.rgyr.dat
aq15.pb.dat
aq15.gb.dat
aq15.sasa.dat

Week 04

Week 04 Lecture: Generating things with ML
Week 04 Lab: Generating Molecular Conformations

Week 05

Week 05 Lecture: Protein Structure Prediction in the Age of Artificial Intelligence
Week 05 Lab: Structure Prediction
work7efy.zip

Week 06

Week 06 Lecture: Molecular Dynamics Concepts 1
Week 06 Lab: Single Particle Langevin Dynamics

Week 07

Week 07 Lecture: Molecular Dynamics Concepts 2
Week 06 Lab: Liquid Argon Simulation
traj_pos_T50.npy
traj_vel_T50.npy
traj_pos_T80.npy
traj_pos_T120.npy
traj_pos_T200.npy

Week 08

Week 8 Lecture: Biomolecular Simulation (Part I)
input.pdb
water.pdb
Biomolecular Simulation (Lab 1)
angiotensin.pdb
Commands to install openmm in Colab

Week 09

Week 09 Lecture: Biomolecular Simulation (Part II)
Week 09 Lab: Analysis of MD trajectories with Markov State Models

Week 10

Week 10: Machine Learning Force Fields
Week 10 Lab: Machine Learning Force Fields (ML-FF)

Week 11

Week 11: Final Project Demo 1 (CHARMM-GUI)
Simulating CHARMM-GUI systems in Google Colab
Simulating CHARMM-GUI systems on HPCC
Week 11: Final Project Demo 2 (Anakin-ASE)

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By Alex Dickson and Michael Feig
© Copyright 2021.