############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # Ubiquitin in a Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../common/protein.psf coordinates ../common/protein.pdb set temperature 310 set outputname protein_wb_eq1 firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../common/par_all27_prot_lipid.inp temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 10. switching on switchdist 8. pairlistdist 12.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 #twoAwayX yes #temperature increment #reassignTemp 25 #reassignIncr 5 #reassignHold 310 #reassignFreq 1000 # 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 # Periodic Boundary Conditions cellBasisVector1 98.27799 0. 0. cellBasisVector2 0. 82.23699 0. cellBasisVector3 0. 0 89.43699 cellOrigin -0.27725 -0.4119 -0.17343 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 #PMEGridSizeX 32 #PMEGridSizeY 32 #PMEGridSizeZ 32 zeroMomentum on # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds #useFlexibleCell no #useConstantArea no # langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100. langevinPistonDecay 50. langevinPistonTemp $temperature # Output outputName $outputname restartfreq 1000 ;# 500steps = every 1ps dcdfreq 1000 xstFreq 1000 outputEnergies 1000 outputPressure 1000 outputTiming 1000 # Fixed Atoms Constraint (set PDB beta-column to 1) #fixedAtoms on #fixedAtomsFile ../common/fixed_protein.pdb #fixedAtomsCol B ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 5000 #run 500 for {set i 0} {$i <= $temperature} {incr i 10} { langevinTemp $i langevinPistonTemp $temperature run 500 } run 5000000 ;# 1ns