mol_model_course_2022

Workshop: Introduction to MD simulations

Description

• Simple hands-on MD simulations in Python + Introduction to Gromacs
• Duration: 90 minutes
• Objectives: be able to
  • Numerically solve simple equations of motion in Python
  • Understand basic algorithm of MD simulations.
  • Understand the organization of Gromacs
  • Understand force field and topology files
  • Prepare files for MD simulation runs
  • Perform energy minimization

Jupyter notebook

• simpleMD.ipynb
• gromacs_intro.ipynb

  Required software and resources

• Access to a Jupyter notebook evironment with Python 3, MDanalysis, nglview and prody libraries
• Access to Newton cluster with Gromacs installed or install Gromacs at your local workstation. See http://www.gromacs.org

Learning resources

• Short Gromacs tutorial https://github.com/intbio/MolModEdu/tree/master/GROMACS/beginner
• Extended Gromacs tutorial https://github.com/intbio/MolModEdu/tree/master/GROMACS/nucl

Assignments

Perform energy minimization of a protein in Gromacs.

1. Plot energy versus step.
2. Compare steepest descent, conjugate gradient and L-BFGS methods.

Suggested problem sets

Each student should take a unique PDB structure at his/her own discretion.

Troubleshooting

• Consult with the seminar protocol/recording
• Ask questions in Slack