############################################################# ## JOB DESCRIPTION ## ############################################################# ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure solvpept3.psf coordinates solvpept3.pdb set temperature 300 set outputname final set velocity velocity set coordinate coordinate set xst celltrajectory firsttimestep 0 # Continuing a job from the restart files #Bincoordinates final.restart.coor #Binvelocities final.restart.vel ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../../../par_modified.inp temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 14. switching on switchdist 11. pairlistdist 18.5 # Integrator Parameters timestep 1.0 ;# 1fs/step #rigidBonds all ;# needed for 2fs steps nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 # Periodic Boundary conditions cellBasisVector1 32.316 0. 0. cellBasisVector2 0. 33.304 0. cellBasisVector3 0. 0 60.096 cellOrigin 26.7246837616 24.504278183 8.62178230286 #extendedSystem final.restart.xsc wrapAll on margin 2.5 # Full electrostatics PME on PMEGridSizeX 34 PMEGridSizeY 34 PMEGridSizeZ 62 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Constant Pressure Control useGroupPressure yes ;# needed for rigidBonds useFlexibleCell yes useConstantArea yes LangevinPiston on LangevinPistonTarget 1.013 ;# in bar LangevinPistonPeriod 200 ;# in fs LangevinPistonDecay 100 LangevinPistonTemp $temperature # set same as langevinTemp # Output outputName $outputname DCDfile $coordinate velDCDfile $velocity XSTfile $xst restartfreq 1000 ;# 1000steps = every 1ps dcdfreq 1000 velDCDfreq 1000 outputEnergies 100 outputPressure 100 XSTfreq 100 DCDUnitCell yes # Fixed Atoms Constraint (set PDB occupancy-column to 1) fixedAtoms on ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 1000 reinitvels $temperature run 5000000 ;# 5ns ÿ