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2026-09-26
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2026-09-25
NAMD minimisation and heating-up script
# # Input files # structure ionized.psf coordinates ionized.pdb parameters par_all27_prot_na.inp paraTypeCharmm on # # Output files & writing frequency for DCD # and restart files # outputname output/heat_out binaryoutput off restartname output/restart restartfreq 1000 binaryrestart yes dcdFile output/heat_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 # temperature 0 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 cellBasisVector1 78.59 00.00 00.00 # <===== CHANGE ME cellBasisVector2 00.00 60.14 00.00 # <===== CHANGE ME cellBasisVector3 00.00 00.00 56.83 # <===== CHANGE ME cellOrigin 0.02 -0.01 2.42 # <===== CHANGE ME # # Fixed atoms for initial heating-up steps # fixedAtoms on fixedAtomsForces on fixedAtomsFile fix_backbone.pdb fixedAtomsCol B # # Restrained atoms for initial heating-up steps # constraints on consRef restrain_ca.pdb consKFile restrain_ca.pdb consKCol B # # Langevin dynamics parameters # langevin on langevinDamping 10 langevinTemp 320 # <===== Check me langevinHydrogen on langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp 320 # <===== Check me useGroupPressure yes ########################################## # The actual minimisation and heating-up # protocol follows. The number of steps # shown below are too small for a real run ########################################## # # run one step to get into scripting mode # minimize 0 # # turn off pressure control until later # langevinPiston off # # minimize nonbackbone atoms # minimize 2000 ;# <===== CHANGE ME output output/min_fix # # min all atoms # fixedAtoms off minimize 2000 ;# <===== CHANGE ME output output/min_all # # heat with CAs restrained # set temp 20; while { $temp < 321 } { ;# <===== Check me langevinTemp $temp run 2000 ;# <===== CHANGE ME output output/heat_ca set temp [expr $temp + 20] } # # equilibrate volume with CAs restrained # langevinPiston on run 10000 ;# <===== CHANGE ME output output/equil_ca # # equilibrate volume without restraints # constraintScaling 0 run 100000 ;# <===== CHANGE ME
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