############################################################# ## JOB DESCRIPTION ## ############################################################# # This is what this job does ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure mypsf.psf coordinates mypdb.pdb set temperature 310 set outputname myoutput # Continuing a job from the restart files if {0} { set inputname myinput binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this! extendedSystem $inputname.xsc proc get_first_ts { xscfile } { set fd [open $xscfile r] gets $fd gets $fd gets $fd line set ts [lindex $line 0] close $fd return $ts } firsttimestep [get_first_ts $inputname.xsc] } else { firsttimestep 0 } ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters 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 {0} { cellBasisVector1 20. 0. 0. cellBasisVector2 0. 20. 0. cellBasisVector3 0. 0 50. cellOrigin 0. 0. 0. } 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 20 #PME (for full-system periodic electrostatics) if {0} { PME yes PMEGridSizeX 32 PMEGridSizeY 32 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 {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 } # Output outputName $outputname restartname $outputname.restart dcdfile $outputname.dcd xstFile $outputname.xst restartfreq 1000 ;# 1000steps = every 1ps dcdfreq 1000 xstFreq 1000 outputEnergies 100 outputPressure 100 # Fixed Atoms Constraint (set PDB beta-column to 1) if {0} { fixedAtoms on fixedAtomsFile myfixedatoms.pdb fixedAtomsCol B } # IMD Settings (can view sim in VMD) if {0} { 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 {0} { minimize 100 reinitvels $temperature } run 500000 ;# 0.5ns