Reference ManualΒΆ
This part of the documentation covers implementation details of GROMACS.
For quick simulation set-up and short explanations, please refer to the User guide.
Help with the installation of GROMACS can be found in the Install guide.
If you want to help with developing GROMACS, your are most welcome to read up on the Developer Guide and continue right away with coding for GROMACS.
- Preface and Disclaimer
- Introduction
- Definitions and Units
- Algorithms
- Periodic boundary conditions
- The group concept
- Molecular Dynamics
- Shell molecular dynamics
- Constraint algorithms
- Simulated Annealing
- Stochastic Dynamics
- Brownian Dynamics
- Energy Minimization
- Normal-Mode Analysis
- Free energy calculations
- Replica exchange
- Essential Dynamics sampling
- Expanded Ensemble
- Parallelization
- Domain decomposition
- Interaction function and force fields
- Topologies
- File formats
- Special Topics
- Free energy implementation
- Potential of mean force
- Non-equilibrium pulling
- Collective variables: the pull code
- Adaptive biasing with AWH
- Enforced Rotation
- Electric fields
- Computational Electrophysiology
- Calculating a PMF using the free-energy code
- Removing fastest degrees of freedom
- Viscosity calculation
- 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
- Run parameters and Programs
- Analysis
- Using Groups
- Looking at your trajectory
- General properties
- Radial distribution functions
- Correlation functions
- Curve fitting in GROMACS
- Mean Square Displacement
- Bonds/distances, angles and dihedrals
- Radius of gyration and distances
- Root mean square deviations in structure
- Covariance analysis
- Dihedral principal component analysis
- Hydrogen bonds
- Protein-related items
- Interface-related items
- Some implementation details
- Averages and fluctuations
- Bibliography