############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # Ubiquitin in a Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# set current restart2 coordinates ionized_min.pdb bincoordinates mdrun_restart1.restart.coor structure ionized.psf binvelocities mdrun_restart1.restart.vel set temperature 310 set outputname mdrun_$current firsttimestep 38194000 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../../olefin_topology_CHARMM36_Nacet/toppar/par_all36_prot.prm parameters ../../olefin_topology_CHARMM36_Nacet/toppar/par_all36_carb.prm parameters ../../olefin_topology_CHARMM36_Nacet/toppar/par_all36_cgenff.prm parameters ../../olefin_topology_CHARMM36_Nacet/par_all36_lipid.prm parameters ../../olefin_topology_CHARMM36_Nacet/toppar/par_all36_na.prm parameters ../../olefin_topology_CHARMM36_Nacet/par_all35_ethers.prm parameters ../../olefin_topology_CHARMM36_Nacet/toppar_water_ions.str #temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 14.0 # Integrator Parameters timestep 0.5 ;# 0.5fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 1/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions cellBasisVector1 41.7 0.0 0.0 cellBasisVector2 0.0 43.6 0.0 cellBasisVector3 0.0 0.0 39.6 cellOrigin 21.1495 -82.0645 23.3275 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 #manual grid definition #PMEGridSizeX 45 #PMEGridSizeY 45 #PMEGridSizeZ 48 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100.0 langevinPistonDecay 50.0 langevinPistonTemp $temperature # Output outputName $outputname binaryoutput no restartfreq 500 ;# 500steps = every 1ps dcdfreq 250 xstFreq 250 outputEnergies 100 outputPressure 100 ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization #minimize 10000 #reinitvels $temperature run 380903000 ;# 190ns