############################################################# ## JOB DESCRIPTION ## ############################################################# # Constant Velocity Pulling ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure system_120a.psf coordinates system_120a.pdb outputName protein_choline_urea_wat_nvt 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 parameters choline-o-sulfate.params # NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file! temperature $temperature if {1} { cellBasisVector1 122.0 0 0 cellBasisVector2 0 122.0 0 cellBasisVector3 0 0 122.0 cellOrigin 61.0 61.0 61.0 } if {0} { set inputname protein_choline_urea_wat_nvt binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel extendedSystem $inputname.restart.xsc } firsttimestep 0 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 restartfreq 1000 #500step = every 1ps dcdfreq 1000 xstFreq 1000 outputEnergies 1000 outputPressure 1000 # Fixed Atoms Constraint (set PDB beta-column to 1) if {1} { fixedAtoms on fixedAtomsFile fixprotein_120a.pdb fixedAtomsCol B } # Minimization if {1} { minimize 100000 reinitvels $temperature } run 100000