structure R7A.psf coordinates R7A.pdb temperature 0 parameters par_all22_prot.inp parameters toppar_all22_prot_heme.str paraTypeCharmm on outputEnergies 12 outputTiming 100 xstFreq 100 dcdFreq 100 restartname nptrest restartfreq 50000 restartsave yes wrapAll on wrapNearest on timestep 1 nonBondedFreq 2 fullElectFrequency 4 stepsPerCycle 20 switching on switchDist 8.5 cutoff 10 pairlistdist 11.5 cellBasisVector1 63.5 0. 0.0 cellBasisVector2 0.0 52.8 0.0 cellBasisVector3 0.0 0 65.6 cellOrigin 40.34 43.10 53.69 # the z dimension is going to shrink so pad sufficiently # the margin could be reduced once the cell is equilibrated margin 5 Pme on PmeGridsizeX 64 PmeGridsizeY 64 PmeGridsizeZ 64 exclude scaled1-4 1-4scaling 1.0 fixedAtoms on fixedAtomsForces on fixedAtomsFile fix_backbone.pdb fixedAtomsCol B constraints on consRef restrain_ca.pdb consKFile restrain_ca.pdb consKCol B langevin on langevinDamping 10 langevinTemp 310 langevinHydrogen no langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp 310 useGroupPressure yes # smaller fluctuations useFlexibleCell yes # allow dimensions to fluctuate independently useConstantRatio yes # fix shape in x-y plane binaryoutput off outputname equil_out # run one step to get into scripting mode minimize 0 # turn off until later langevinPiston off # minimize nonbackbone atoms minimize 10000 output min_fix # min all atoms fixedAtoms off minimize 10000 output min_all # heat with CAs restrained # langevin on run 3000 output heat # equilibrate volume with CAs restrained langevinPiston on run 5000 output equil_ca # equilibrate volume without restraints constraintScaling 0 run 10000 # NVT equilibration # langevin off langevinPiston off run 50000 ;# run 50000 output equil_nvt # NPT equilibration langevinPiston on run 750000 ;# run 7500000 output equil_npt