# ApoA1 # # select simulation options # set do_langevin 1 ;# Using Langevin thermostat? set do_stochres 0 ;# Using stochastic rescaling thermostat? set do_piston 1 ;# Using Langevin piston, along with a thermostat? # output steps # (for CUDA do not perform output more frequently than every 500 steps) # set outsteps 500 ;# output interval set steps 10000 ;# number of simulation steps # always do PME set do_pme 1 ;# Using PME? # set temperature set temp 298 ;# temperature in Kelvin # # input files # coordinates apoa1.pdb structure apoa1.psf parameters par_all22_prot_lipid.xplor parameters par_all22_popc.xplor # # simulation parameters # seed 74269 # setting initial velocities to temperature # temperature $temp # system-dependent periodic cell definition # cellBasisVector1 108.8612 0.0 0.0 cellBasisVector2 0.0 108.8612 0.0 cellBasisVector3 0.0 0.0 77.758 cellOrigin 0.0 0.0 0.0 # non-bonded force parameters # exclude scaled1-4 1-4scaling 1.0 switching on switchdist 10 cutoff 12 pairlistdist 13.5 margin 0 # apply aggressive multiple time stepping # timestep 2.0 nonbondedFreq 1 fullElectFrequency 2 stepspercycle 20 rigidbonds all useSettle on # temperature control options # if { $do_langevin } { # constant temperature langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temp langevinHydrogen off ;# don't couple langevin bath to hydrogens } elseif { $do_stochres } { stochRescale on stochRescalePeriod 0.5 stochRescaleFreq 20 stochRescaleTemp $temp } # pressure control options # also need thermostat # if { $do_piston } { # constant pressure (variable volume) langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100. langevinPistonDecay 50. langevinPistonTemp $temp useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no } # PME grid sizes based on periodic cell sizes # if { $do_pme } { PME on PMEGridSizeX 108 PMEGridSizeY 108 PMEGridSizeZ 80 } # output parameters # outputName apoa1-output outputTiming $outsteps outputEnergies $outsteps ldbalancer none numsteps $steps