set sys mos2_2.6+dna_grad set this ${sys}_eq set last ${sys}_min numsteps 600000 structure ${sys}_ions.psf coordinates ${sys}_ions.pdb outputName $this binCoordinates $last.restart.coor #binVelocities $last.restart.vel temperature 295 extendedSystem $last.restart.xsc # temperature control langevin on langevinTemp 295 langevinDamping 5 langevinHydrogen off # pressure control useGroupPressure on useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 langevinPistonTemp 295 langevinPistonDecay 300 langevinPistonPeriod 300 # parameters parameters ../c32b1/toppar/par_all27_prot_lipid.prm parameters ../c32b1/toppar/par_all27_na.prm parameters ./par_lj_MoS2.inp paraTypeCharmm on exclude scaled1-4 1-4scaling 1.0 switching on switchDist 10 cutoff 12 pairListDist 14 # integraion rigidBonds all timestep 2 nonBondedFreq 1 fullElectFrequency 2 stepsPerCycle 10 # output binaryOutput yes binaryRestart yes #wrapAll yes wrapNearest yes comMotion yes outputEnergies 1000 outputPressure 1000 outputTiming 1000 xstFreq 1000 dcdFreq 5000 restartFreq 5000 # electrostatics pme on pmeGridSizeX 96 pmeGridSizeY 96 pmeGridSizeZ 240 # external forces constraints on consKCol B consRef ${sys}_restrain.pdb consKFile ${sys}_restrain.pdb fixedAtoms on fixedAtomsFile ${sys}_fixed.pdb fixedAtomsCol B