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2024-12-23
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2024-12-22
NAMD restart2 script
# # Input files # structure ionized.psf coordinates heat_out.coor bincoordinates restart2.coor binvelocities restart2.vel extendedSystem restart2.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/restart3 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 80 # <===== CHANGE ME PmeGridsizeY 64 # <===== 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 1203000 # <===== CHANGE ME run 3943000 ;# <===== CHANGE ME