Special TopicsΒΆ
This section covers some of the more specialized topics concerning the use of GROMACS for specific scientific problems.
- Free energy implementation
- Potential of mean force
- Non-equilibrium pulling
- The pull code
- Adaptive biasing with AWH
- Enforced Rotation
- Fixed Axis Rotation
- Pivot-Free Isotropic Potential
- Parallel Motion Potential Variant
- Pivot-Free Parallel Motion Potential
- Radial Motion Potential
- Pivot-Free Radial Motion Potential
- Radial Motion 2 Alternative Potential
- Pivot-Free Radial Motion 2 Potential
- Flexible Axis Potential
- Flexible Axis 2 Alternative Potential
- Angle of Rotation Groups: Fixed Axis
- Angle of Rotation Groups: Flexible Axis
- Angle Determination by Searching the Energy Minimum
- Torque
- Electric fields
- Computational Electrophysiology
- Calculating a PMF using the free-energy code
- Removing fastest degrees of freedom
- Viscosity calculation
- Tabulated interaction functions
- Mixed Quantum-Classical simulation techniques
- MiMiC Hybrid Quantum Mechanical/Molecular Mechanical simulations
- Using VMD plug-ins for trajectory file I/O
- Interactive Molecular Dynamics
- Embedding proteins into the membranes