Gromacs on EUREKA

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

Contents

• Pre-Simulation
  • Generating Topologies for an Arbitrary PDB
  • Creating Custom Force Fields and Residue Entries
  • 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?