# Minimization and Equilibration of # A memberane bilayer having POPC (28 mols) and POPS (2 mols) and 2 Na+ atoms. #Input amber yes parmfile final.prmtop ambercoor final.inpcrd readexclusions no scnb 2 temperature 300 cwd POPC_POPS # Minimisation minimize 100 reinitvels 300 run 2000 # force field params exclude sc1aled1-4 1-4scaling 0.5 switching on switchdist 8.0 cutoff 12.0 pairlistdist 13.5 stepspercycle 20 # Periodic Boundary Conditions cellBasisVector1 35. 0. 0. cellBasisVector2 0. 39. 0. cellBasisVector3 0. 0 88. cellOrigin 1.8 1. -8.3 # Configuration parameters numsteps 1000000 timestep 1.0 firsttimestep 0 fullElectFrequency 2 #Constant Temperature Control langevin on langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp 300 langevinHydrogen off ;# don't couple langevin bath to hydrogens # Constant Pressure Control useGroupPressure yes ;# needed for rigid bonds useFlexibleCell yes ;# no for water box, yes for membrane useConstantArea no ;# no for water box, maybe for membrane langevinPiston on langevinPistonTarget 1.01325 ;# pressure in bar -> 1 atm langevinPistonPeriod 100. ;# oscillation period around 100 fs langevinPistonDecay 50. ;# oscillation decay time of 50 fs langevinPistonTemp 300 ;# coupled to heat bath # full electrostatics PME on PMEGridSizeX 36 PMEGridSizeY 40 PMEGridSizeZ 90 # output params outputname output binaryoutput no DCDfreq 500 DCDfile output xstFreq 500 restartfreq 500 outputEnergies 10 outputPressure 10 outputMomenta 10