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Constraints and Restraints
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NAMD 2.0 User's Guide
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NAMD configuration parameters
Contents
Additional Simulation Parameters
Constraints and Restraints
Harmonic constraint parameters
Fixed atoms parameters
Energy Minimization
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
Moving Constraints
Rotating Constraints
Steered Molecular Dynamics (SMD)
Changing direction of reference position movement
Choice of new direction
Resetting the applied force
Output
Parameters
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
namd@ks.uiuc.edu
