############################################################# ## JOB DESCRIPTION ## ############################################################# # This is what this job does ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure 1a34_full_autopsf_modified.psf coordinates 1a34_full_autopsf_modified.pdb outputName out set temperature 298 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all27_na.prm parameters par_all22_prot.inp # NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file! temperature $temperature # Periodic Boundary conditions # NOTE: Do not set the periodic cell basis if you have also # specified an .xsc restart file! if {0} { cellBasisVector1 200. 0. 0. cellBasisVector2 0. 200. 0. cellBasisVector3 0. 0. 200. cellOrigin 100. 100. 100. } wrapWater on wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 1.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 2 fullElectFrequency 4 stepspercycle 10 #PME (for full-system periodic electrostatics) if {0} { PME yes PMEGridSizeX 205 PMEGridSizeY 205 PMEGridSizeZ 205 } # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens # Constant Pressure Control (variable volume) if {0} { useGroupPressure yes ;# needed for 2fs steps useFlexibleCell no ;# 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 100. langevinPistonDecay 50. langevinPistonTemp $temperature } restartfreq 500 ;# 500steps = every 1ps dcdfreq 500 xstFreq 500 outputEnergies 500 outputPressure 500 outputtiming 500 ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Put here any custom parameters that are specific to # this job (e.g., SMD, TclForces, etc...) ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization #if {0} { #minimize 100 #reinitvels $temperature #} minimize 10000 run 75000 ;# 150ps