structure popc_mlt_ion.psf coordinates popc_mlt_ion.pdb outputName production4 set temperature 310 set inputname ../EQ3/eq3 binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel extendedSystem $inputname.restart.xsc firsttimestep 1253000 paraTypeCharmm on parameters par_all27_prot_lipid.prm COMmotion no wrapWater on wrapAll on exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 timestep 2.0 rigidBonds all nonbondedFreq 1 fullElectFrequency 2 stepspercycle 20 PME yes PMEGridSizeX 54 PMEGridSizeY 54 PMEGridSizeZ 90 langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature useGroupPressure yes ;# needed for 2fs steps useFlexibleCell yes ;# no for water box, yes for membrane useConstantArea no ;# no for water box, yes for membrane langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 200. langevinPistonDecay 50. langevinPistonTemp $temperature restartfreq 5000 dcdfreq 5000 xstFreq 5000 outputEnergies 250 outputPressure 250 margin 5 run 40000000