structure test.psf coordinates test.pdb temperature 0 parameters par_all27_prot_lipid.inp paraTypeCharmm on outputEnergies 500 outputTiming 500 xstFreq 500 dcdFreq 500 wrapAll on wrapNearest on rigidbonds all timestep 2 nonBondedFreq 2 fullElectFrequency 4 stepsPerCycle 20 exclude scaled1-4 1-4scaling 1.0 switching on switchDist 8 cutoff 9 pairlistdist 11.5 cellBasisVector1 65.00 00.00 00.00 cellBasisVector2 00.00 70.00 00.00 cellBasisVector3 00.00 00.00 65.00 cellOrigin -6.91 -12.71 -10.24 Pme on PmeGridsizeX 70 PmeGridsizeY 75 PmeGridsizeZ 70 fixedAtoms on fixedAtomsForces on fixedAtomsFile test_fix_backbone.pdb fixedAtomsCol B constraints on consRef test_restrain_ca.pdb consKFile test_restrain_ca.pdb consKCol B langevin on langevinDamping 10 langevinTemp 298 langevinHydrogen no langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp 298 useGroupPressure yes # smaller fluctuatios binaryoutput off outputname test_equil # run one step to get into scripting mode minimize 0 # turn off until later langevinPiston off # minimize nonbackbone atoms minimize 1000 output test_min_fix # min all atoms fixedAtoms off minimize 1000 output test_min_all # heat with CAs restrained # langevin on run 15000 output test_heat # equilibrate volume with CAs restrained langevinPiston on run 10000 output test_equil_ca # equilibrate volume without restraints constraintScaling 0 run 300000