Workshop: Introduction to MD simulations
- 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
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
Perform energy minimization of a protein in Gromacs.
- Plot energy versus step.
- 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.
- Consult with the seminar protocol/recording
- Ask questions in Slack