# STMV # # 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 100 steps) # set outsteps 100 ;# output interval set steps 2000 ;# number of simulation steps # always do PME set do_pme 1 ;# Using PME? # set temperature set temp 298 ;# temperature in Kelvin # # input files # coordinates stmv.pdb structure stmv.psf paraTypeCharmm on parameters par_all27_prot_na.inp # # simulation parameters # seed 74269 # setting initial velocities to temperature # temperature $temp # system-dependent periodic cell definition # cellBasisVector1 216.832 0. 0. cellBasisVector2 0. 216.832 0. cellBasisVector3 0. 0 216.832 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 216 PMEGridSizeY 216 PMEGridSizeZ 216 } # output parameters # outputName stmv-output outputTiming $outsteps outputEnergies $outsteps ldbalancer none numsteps $steps