#JOB DESCRIPTION ## ############################################################# # bilayer equilibration ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure mem.psf coordinates mem.pdb #binvelocities min_mem.vel set start_temperature 0 set hold_temperature $temp set outputname min_mem.md firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS # Input paraTypeCharmm on parameters par.prm temperature 0 # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 #Cutoff-2 pairlistdist 14.0 #Cutoff+2 stepspercycle 10 margin 2.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 useSettle on ;#If rigid bonds are enabled #use #non-interactive SETTLE alg to keep waters rigid # Constant Temperature Control #langevin off ;# do langevin dynamics #langevinDamping 5 ;# damping coefficient (gamma) of 5/ps #langevinHydrogen no ;# don't couple langevin bath to hydrogens #langevinTemp $temp ;#langevin temperature is #defined in protocol section #Affects the output. Wrapping does not affect the simulation. wrapWater on wrapAll on #Pressure Control useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100. langevinPistonDecay 50. langevinPistonTemp $temp # Periodic Boundary Conditions cellBasisVector1 79.72 0 0 cellBasisVector2 0 81.60 0 cellBasisVector3 0 0 98.1 cellOrigin 0.0 0.0 0.0 #PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 ;#Using good default. Let NAMD set the grid. PMEGridSizeX 80 PMEGridSizeY 90 PMEGridSizeZ 100 # Output binaryoutput off outputName $output restartfreq 2500 dcdfreq 2500 xstFreq 2500 outputEnergies 2500 outputPressure 2500 ############################################################# ## EXTRA PARAMETERS ## ############################################################# constraints off ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization # ( 10 ps ) minimize 5000 #RELAXATION PROTOCOL 350000 steps # 14 frames (dcdfreq=2500) # 700 ps (timestep=2fs) Heat +1K in 0.4ps for { set TEMP 0 } { $TEMP < $temp } { incr TEMP 1 } { langevinTemp $TEMP reinitvels $temp run 200 } #Adjust environment to final conditions langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) #of 5/ps langevinTemp $temp reinitvels $temp #Constraints release protocol #Free dynamics for 50 ps constraintScaling 0 run 25000