structure depc_xplor.psf coordinates read_200_depc_bilayer_w_water.pdb set temperature 303.15 ;# target temperature used several times below # continuing a run set inputname equil.restart ;# only need to edit this in one place! outputName prod ;# base name for output from this run binCoordinates $inputname.coor ;# coordinates from last run (binary) binVelocities $inputname.vel ;# velocities from last run (binary) extendedSystem $inputname.xsc ;# cell dimensions from last run firsttimestep 0 ;# last step of previous run numsteps 1000 ;# run stops when this step is reached restartfreq 500 ;# 500 steps = every 1ps dcdfreq 500 dcdUnitCell yes ;# the file will contain unit cell info in the style of charmm dcd files xstFreq 500 outputEnergies 25 ;# 100 steps = every 0.2 ps outputTiming 500 ;# shows time per step and time to completion #outputPressure 100 ;# # Force-Field Parameters paraTypeCharmm on parameters par_all32_lipid_1a.inp # These are specified by CHARMM exclude scaled1-4 1-4scaling 1.0 switching on # You have some freedom choosing the cutoff cutoff 10. ;# may use smaller, maybe 10., with PME switchdist 8. ;# cutoff - 2. # Promise that atom won't move more than 2A in a cycle pairlistdist 12. ;# cutoff + 2. stepspercycle 20 ;# 20 redo pairlists every ten steps firstldbstep 50 ldbperiod 100 # Integrator Parameters timestep 2.0 ;# fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 ;# nonbonded forces every step fullElectFrequency 1 ;# 2 PME only every other step # Constant Temperature Control reassignFreq 500 reassignTemp $temperature wrapWater on ;# wrap water to central cell wrapAll on ;# wrap other molecules too wrapNearest off ;# use for non-rectangular cells #PME (for full-system periodic electrostatics) PME yes PMEGridSizeX 128 ; PMEGridSizeY 128 ; PMEGridSizeZ 128 ; # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigid bonds useFlexibleCell yes ;# no for water box, yes for membrane useConstantArea yes ;# 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 $temperature ;# coupled to heat bath run 1000 ;