Gromacs on EUREKA

This wiki provides instructions on general and EUREKA-specific Gromacs methods

Contents

• 1. Input preparation
  • a) Generating Topologies for an Arbitrary PDB-Generating-Topologies-for-an-Arbitrary-PDB)
  • b) Unit Cells and Solvation
  • c) Neutralisation
• 2. Energy Minimisation and Equilibration
  • a) Energy minimisation
  • b) NVT Equilibration
  • c) NPT Equilibration
• 3. Running the Dynamics
• 4. Analysis
  • a) Quantifying average motion
  • b) Animating the system
  • c) PLUMED?