############################################################# ## JOB DESCRIPTION ## ############################################################# # Equilibration of 500 molecules of ethanol ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../common/final.psf coordinates ../02_Heating/final_heat.coor extendedSystem ../02_Heating/final_heat.xsc set temperature 300 set outputname final_eq set restart 0 # Continuing a job from the restart files if {$restart} { set inputname $outputname Coordinates ../$inputname.restart.coor Velocities ../$inputname.restart.vel ;# remove the "temperature" entry if you use this! extendedSystem ../$inputname.restart.xsc } firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../common/final.params if {$restart-1} { temperature $temperature } # Force-Field Parameters exclude scaled1-4 1-4scaling 0.5 cutoff 12.0 switching on switchdist 10.5 pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# 1fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 vdwGeometricSigma yes fullElectFrequency 2 stepspercycle 20 pairlistsperCycle 2 # Periodic Boundary Conditions if {0} { cellBasisVector1 52.8 0. 0.0 cellBasisVector2 0.0 52.6 0.0 cellBasisVector3 0.0 0 103.7 cellOrigin 25.0 25.0 47.0 # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 #manual grid definition #PMEGridSizeX 45 #PMEGridSizeY 45 #PMEGridSizeZ 100 } wrapAll on # Constant Temperature Control if {1} { langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 1/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens } # Constant Pressure Control (variable volume) if {1} { useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100.0 langevinPistonDecay 50.0 langevinPistonTemp $temperature } # Fixed Atoms Constraint (set PDB beta-column to 1) if {0} { fixedAtoms on #fixedAtomsForces on #Is it necessary? fixedAtomsFile ../../02_Heating/IL20-Mixed_heat.coor 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? } # Output outputName $outputname restartfreq 10000 ;# 10000 steps = every 20 ps dcdfreq 5000 outputEnergies 500 outputPressure 500 binaryoutput no binaryrestart no ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Equilibration seed 1010 # Random number seed used to generate initial Maxwell distribution of velocities numsteps 1000000 # Number of integration steps