Gromacs on EUREKA

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

Contents

• Input preparation
  • Generating Topologies for an Arbitrary PDB
  • Unit Cells and Solvation
  • Neutralisation
• Energy Minimisation and Equilibration
  • Energy minimisation
  • NVT Equilibration
  • NPT Equilibration
• Molecular Dynamics
• Analysis
  • Quantifying average motion
  • Animating the system
  • PLUMED?