67 lines
3.1 KiB
Plaintext
67 lines
3.1 KiB
Plaintext
# Simulation Configuration File for NAMD
|
|
# --------------------------------------
|
|
|
|
# Input and output files
|
|
structure enzyme.psf # PSF file of the enzyme
|
|
coordinates enzyme.pdb # PDB file of the enzyme
|
|
outputName output/simulation # Prefix for output files
|
|
|
|
# Force field parameters
|
|
paraTypeCharmm on # Use CHARMM force field
|
|
parameters charmm36.prm # Parameter file for CHARMM36 force field
|
|
temperature 300 # Temperature in Kelvin
|
|
|
|
# Periodic boundary conditions (Assumes cubic box, modify as needed)
|
|
cellBasisVector1 100.0 0.0 0.0
|
|
cellBasisVector2 0.0 100.0 0.0
|
|
cellBasisVector3 0.0 0.0 100.0
|
|
cellOrigin 0.0 0.0 0.0
|
|
wrapAll on
|
|
|
|
# PME (Particle Mesh Ewald) for long-range electrostatics
|
|
PME yes # Enable PME for electrostatics
|
|
PMEGridSizeX 96 # Grid size for PME (adjust to fit box size)
|
|
PMEGridSizeY 96
|
|
PMEGridSizeZ 96
|
|
|
|
# Integrator parameters
|
|
timestep 2.0 # 2 fs per step
|
|
nonbondedFreq 1 # Non-bonded interactions calculated every step
|
|
fullElectFrequency 2 # Full electrostatics evaluated every 2 steps
|
|
stepspercycle 20 # Grouping of integration steps
|
|
|
|
# Temperature control (Langevin dynamics)
|
|
langevin on # Use Langevin dynamics for temperature control
|
|
langevinDamping 1.0 # Damping coefficient (1/ps)
|
|
langevinTemp 300 # Target temperature in Kelvin
|
|
langevinHydrogen off # Exclude hydrogen atoms from Langevin dynamics
|
|
|
|
# Pressure control (Langevin piston for NPT ensemble)
|
|
useGroupPressure yes # More stable, accurate Langevin piston
|
|
useFlexibleCell no # Keep box shape fixed
|
|
useConstantArea no
|
|
langevinPiston on
|
|
langevinPistonTarget 1.01325 # Target pressure in bar (1 atm)
|
|
langevinPistonPeriod 100.0 # Piston oscillation period (fs)
|
|
langevinPistonDecay 50.0 # Damping timescale (fs)
|
|
langevinPistonTemp 300 # Piston temperature (K)
|
|
|
|
# Minimization
|
|
minimize 1000 # Minimization steps
|
|
|
|
# Equilibration phase
|
|
reassignFreq 1000 # Reassign temperature every 1000 steps
|
|
reassignTemp 300 # Set initial temperature for equilibration
|
|
reassignIncr 1.0 # Increase temperature slowly
|
|
reassignHold 300 # Hold at 300 K
|
|
|
|
# Production phase (run)
|
|
run 500000 # Number of steps for production run (1 ns with 2 fs timestep)
|
|
|
|
# Output settings
|
|
restartfreq 1000 # Save restart files every 1000 steps
|
|
dcdfreq 1000 # Save trajectory data every 1000 steps
|
|
xstFreq 1000 # Save extended system data (for periodic boundary conditions)
|
|
outputEnergies 100 # Output energy data every 100 steps
|
|
|