############################################################# ## JOB DESCRIPTION ## ############################################################# # This is what this job does ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../../psf/ionized_wb.psf coordinates ../../psf/ionized_wb.pdb outputName hemo_wb_eq set temperature 310 # Continuing a job from the restart files if {1} { set inputname hemo_wb binCoordinates ../output1/$inputname.restart.coor #binVelocities ../psf/$inputname.restart.vel ;# remove the "temperature" entry if you use this! extendedSystem ../output1/$inputname.restart.xsc } firsttimestep 5500 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../../psf/par_all27_prot_lipid.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 {1} { #cellBasisVector1 90.2748 0. 0. #cellBasisVector2 0. 74.238 0. #cellBasisVector3 0. 0 81.4690 # #cellOrigin -0.2554 -0.320 -0.0591 #} wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 #PME (for full-system periodic electrostatics) if {1} { PME yes PMEGridSpacing 1.0 #PMEGridSizeX 64 #PMEGridSizeY 64 #PMEGridSizeZ 64 } # 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 {1} { 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 # Fixed Atoms Constraint (set PDB beta-column to 1) #if {1} { #fixedAtoms on #fixedAtomsFile myfixedatoms.pdb #fixedAtomsCol B #} # IMD Settings (can view sim in VMD) #if {1} { #IMDon on #IMDport 3000 ;# port number (enter it in VMD) #IMDfreq 1 ;# send every 1 frame #IMDwait no ;# wait for VMD to connect before running? #} ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Put here any custom parameters that are specific to # this job (e.g., SMD, TclForces, etc...) ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization #if {1} { #minimize 100 #reinitvels $temperature #} run 5000 ;# 10ps