# # Input files # structure ionized.psf coordinates heat_out.coor velocities heat_out.vel extendedSystem heat_out.xsc parameters par_all27_prot_na.inp paraTypeCharmm on # # Output files & writing frequency for DCD # and restart files # outputname output/equi_out binaryoutput off restartname output/restart restartfreq 1000 binaryrestart yes dcdFile output/equi_out.dcd dcdFreq 200 # # Frequencies for logs and the xst file # outputEnergies 20 outputTiming 200 xstFreq 200 # # Timestep & friends # timestep 2.0 stepsPerCycle 8 nonBondedFreq 2 fullElectFrequency 4 # # Simulation space partitioning # switching on switchDist 10 cutoff 12 pairlistdist 13.5 # # Basic dynamics # COMmotion no dielectric 1.0 exclude scaled1-4 1-4scaling 1.0 rigidbonds all # # Particle Mesh Ewald parameters. # Pme on PmeGridsizeX 81 # <===== CHANGE ME PmeGridsizeY 60 # <===== CHANGE ME PmeGridsizeZ 60 # <===== CHANGE ME # # Periodic boundary things # wrapWater on wrapNearest on wrapAll on # # Langevin dynamics parameters # langevin on langevinDamping 1 langevinTemp 320 # <===== Check me langevinHydrogen on langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 200 langevinPistonDecay 500 langevinPistonTemp 320 # <===== Check me useGroupPressure yes firsttimestep 146000 # <===== CHANGE ME run 1000000 ;# <===== CHANGE ME