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Constraints and Restraints
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NAMD 2.5b1 User's Guide
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NAMD configuration parameters
Contents
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
Steered Molecular Dynamics (SMD)
Output
Parameters
Interactive Molecular Dynamics (IMD)
Tcl interface
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
Alchemical Free Energy Perturbation Calculations
Introduction and theoretical background
Implementation of free energy perturbation in NAMD
Examples of input files for running FEP alchemical calculations
Description of FEP simulation output
Locally Enhanced Sampling
Structure Generation
Simulation
namd@ks.uiuc.edu
