# 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