Special Topics#
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
- Collective variables: 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
- Shear simulations
- Tabulated interaction functions
- Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface
- MiMiC Hybrid Quantum Mechanical/Molecular Mechanical simulations
- Using VMD plug-ins for trajectory file I/O
- Interactive Molecular Dynamics
- Embedding proteins into the membranes
- Applying forces from three-dimensional densities
- Overview
- Usage
- The simulated density and its force contribution
- The density similarity measure and its force contribution
- Declaring regions to fit
- Performance
- Applying force every N-th step
- Combining density-guided simulations with pressure coupling
- Periodic boundary condition treatment
- The reference density map format
- Output
- Adaptive force constant scaling
- Mapping input structure to density data with affine transformations
- Future developments