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
  • Entropic effects
• Non-equilibrium pulling
• Collective variables: the pull code
  • Definition of the center of mass
  • Definition of the pull direction
  • Definition of the angle and dihedral pull geometries
  • The transformation pull coordinate
  • Limitations
• Adaptive biasing with AWH
  • Basics of the method
  • The free energy update
  • Applying the bias to the system
  • The covering criterion
  • Exit from the initial stage
  • Setting the initial update size
  • Estimating errors
  • Tips for efficient sampling
• 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
  • Boundary conditions
• Computational Electrophysiology
  • Usage
  • Multimeric channels
• Calculating a PMF using the free-energy code
• Removing fastest degrees of freedom
  • Hydrogen bond-angle vibrations
• Viscosity calculation
• Shear simulations
• Tabulated interaction functions
  • Cubic splines for potentials
  • User-specified potential functions
• Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface
  • Overview
  • Software prerequisites
  • Limitations in simulation techniques
  • Usage
  • Choosing atoms for QM calculation
  • Supported QM methods
  • Providing your own CP2K input file
  • Changing names of CP2K files
  • Output
  • Future developments
• MiMiC Hybrid Quantum Mechanical/Molecular Mechanical simulations
  • Overview
  • Application coupling model
  • Software prerequisites
  • Usage
  • Preparing the input file for GROMACS
  • Preparing the input file for CPMD
  • Running a MiMiC QM/MM simulation
  • Known Issues
• Using VMD plug-ins for trajectory file I/O
• Interactive Molecular Dynamics
  • Simulation input preparation
  • Starting the simulation
  • Connecting from VMD
• 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
• Collective Variable simulations with the Colvars module
  • Using Colvars
  • Configuration files for input
  • Colvars output files
  • Colvars checkpointing
• Using PLUMED
  • Configuration files for input
  • Limitations
• Neural Network Potentials
  • Hybrid NNP/MM Simulations
  • Software Prerequisites
  • Usage