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Constraints and Restraints
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NAMD 2.6 User's Guide
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NAMD configuration parameters
Contents
Index
Additional Simulation Parameters
Subsections
Constraints and Restraints
Harmonic constraint parameters
Fixed atoms parameters
Energy Minimization
Conjugate gradient parameters
Velocity quenching parameters
Temperature Control and Equilibration
Langevin dynamics parameters
Temperature coupling parameters
Temperature rescaling parameters
Temperature reassignment parameters
Boundary Conditions
Spherical harmonic boundary conditions
Cylindrical harmonic boundary conditions
Periodic boundary conditions
Pressure Control
Berendsen pressure bath coupling
Nosé-Hoover Langevin piston pressure control
Applied Forces and Analysis
Constant Forces
External Electric Field
Moving Constraints
Rotating Constraints
Targeted Molecular Dynamics (TMD)
Steered Molecular Dynamics (SMD)
Output
Parameters
Interactive Molecular Dynamics (IMD)
Tcl Forces and Analysis
Tcl Boundary Forces
Free Energy of Conformational Change Calculations
User-Supplied Conformational Restraints
Free Energy Calculations
Options for Conformational Restraints
Options for ATOM Specification
Options for Potential of Mean Force Calculation
Examples
Appendix
Adaptive Biasing Force Calculations
Introduction and theoretical background
Using the NAMD implementation of the adaptive biasing force method
Parameters for ABF simulations
Including restraints in ABF simulations
Important recommendations when running ABF simulations
Example of input file for computing potentials of mean force
Alchemical Free Energy Perturbation Calculations
Introduction and theoretical background
Implementation of free energy perturbation in NAMD
Example of an input file for running FEP alchemical transformations
Description of FEP simulation output
Locally Enhanced Sampling
Structure Generation
Simulation
Pair Interaction Calculations
Pressure Profile Calculations
Replica Exchange Simulations
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