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Boundary Conditions
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NAMD 3.0.3 User's Guide
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Configuration Parameters
Contents
Index
Standard Minimization and Dynamics Parameters
Subsections
Boundary Conditions
Periodic boundary conditions
Spherical harmonic boundary conditions
Cylindrical harmonic boundary conditions
Energy Minimization
Conjugate gradient parameters
Velocity quenching parameters
Dynamics
Timestep parameters
Initialization
Conserving momentum
Multiple timestep parameters
Temperature Control and Equilibration
Langevin dynamics parameters
Temperature coupling parameters
Stochastic velocity rescaling parameters
Temperature rescaling parameters
Temperature reassignment parameters
Lowe-Andersen dynamics parameters
Pressure Control
Berendsen pressure bath coupling
Nosé-Hoover Langevin piston pressure control
Monte Carlo barostat
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