Gromacs on EUREKA

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

Contents

• Pre-Simulation
  • Generating Topologies for an Arbitrary PDB
    • Finding structures
    • Selecting a Force Field
    • Selecting Termini
    • Fixing errors
      • Atom AAA in residue BBC was not found in rtp entry DD with E atoms
  • Creating Custom Force Fields and Residue Entries
    • Creating a Copy of a Force Field
    • Understanding Residue Entries
  • Position Restraints
  • Unit Cells and Solvation
  • Neutralisation
• 2. Energy Minimisation and Equilibration
  • a) Energy minimisation
  • b) NVT Equilibration
  • c) NPT Equilibration
• 3. Running the Dynamics
• 4. Analysis
  • Investigating hydrogen bonding Investigating hydrogen bonding
  • Getting, setting, and shifting CoM's in a PDB
  • a) Quantifying average motion
  • b) Animating the system
  • c) PLUMED?