############################################################# ## JOB DESCRIPTION ## ############################################################# # Constant Velocity Pulling ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure system.psf coordinates system.pdb outputName protein_choline_urea_wat_npt_eq set temperature 310 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all36_carb.prm parameters par_all36_cgenff.prm parameters par_all36_lipid.prm parameters par_all36_na.prm parameters par_all36_prot.prm parameters toppar_all36_carb_glycolipid.str parameters toppar_all36_lipid_bacterial.str parameters toppar_all36_lipid_cholesterol.str parameters toppar_water_ions.str # NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file! #temperature $temperature if {0} { cellBasisVector1 0.0 0 0 cellBasisVector2 0 0.0 0 cellBasisVector3 0 0 0.0 cellOrigin 0.0 0 0.0 } if {1} { set inputname protein_choline_urea_wat_nvt binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel extendedSystem $inputname.restart.xsc } firsttimestep 200000 wrapWater on wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12 switching on switchdist 10 pairlistdist 14 # Integrator Parameters timestep 2.0 # 2fs/step rigidBonds all # needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on # do langevin dynamics langevinDamping 5 # damping coefficient (gamma) of 5/ps langevinTemp 300 langevinHydrogen no # don't couple langevin bath to hydrogens # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 # Constant Pressure Control (variable volume) if {1} { useGroupPressure yes # needed for 2fs steps useFlexibleCell no # no for water box, yes for membrane useConstantArea no # no for water box, yes for membrane langevinPiston on langevinPistonTarget 1.0325 # in bar -> 1 atm langevinPistonPeriod 100 langevinPistonDecay 50 langevinPistonTemp 300 } restartfreq 1000 # 500step = every 1ps dcdfreq 1000 xstFreq 1000 outputEnergies 1000 outputPressure 1000 # Fixed Atoms Constraint (set PDB beta-column to 1) if {0} { fixedAtoms on fixedAtomsFile fixprotein_120a.pdb fixedAtomsCol B } # Minimization if {1} { #minimize xxxx #reinitvels $temperature } run 500000