GROMACS Reference Manual 2018.3
User Manual:
Open the PDF directly: View PDF
Page Count: 270 [warning: Documents this large are best viewed by clicking the View PDF Link!]
- Introduction
- Definitions and Units
- Algorithms
- Introduction
- 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
- Implicit solvation
- Interaction function and force fields
- Non-bonded interactions
- Bonded interactions
- Bond stretching
- Morse potential bond stretching
- Cubic bond stretching potential
- FENE bond stretching potential
- Harmonic angle potential
- Cosine based angle potential
- Restricted bending potential
- Urey-Bradley potential
- Bond-Bond cross term
- Bond-Angle cross term
- Quartic angle potential
- Improper dihedrals
- Proper dihedrals
- Tabulated bonded interaction functions
- Restraints
- Polarization
- Free energy interactions
- Methods
- Virtual interaction sites
- Long Range Electrostatics
- Long Range Van der Waals interactions
- Force field
- Topologies
- Special Topics
- Free energy implementation
- Potential of mean force
- Non-equilibrium pulling
- 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
- Mixed Quantum-Classical simulation techniques
- Using VMD plug-ins for trajectory file I/O
- Interactive Molecular Dynamics
- Embedding proteins into the membranes
- 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
- Index