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