# MD simulation for 10 ns (at T=550K, constant Volume) # input structure rbp_ions.psf coordinates sim_fixprot.pdb; #shall I use emin.pdb or sim_fixprot.pdb binCoordinates sim_fixprot.coor ;# coordinates from last run (binary) extendedSystem sim_fixprot.xsc ;# cell dimensions from last run parameters par_all27_prot_lipid_na.inp paratypecharmm on # output # *** specify the correct folder here *** set output sim_free outputname $output dcdfile ${output}.dcd xstFile ${output}.xst dcdfreq 2000 xstFreq 2000 binaryoutput yes binaryrestart yes outputEnergies 100 restartfreq 100000 fixedAtoms off # Basic dynamics exclude scaled1-4 1-4scaling 1 COMmotion no dielectric 1.0 # Simulation space partitioning switching on switchdist 9 cutoff 10 pairlistdist 12 # Multiple timestepping firsttimestep 0 timestep 1 stepspercycle 20 nonbondedFreq 2 fullElectFrequency 4 # Temperature control set temperature 550 temperature $temperature; # initial temperature # Langevin Dynamics langevin on; # do langevin dynamics langevinDamping 5; # damping coefficient (gamma) of 1/ps langevinTemp $temperature; # bath temperature langevinHydrogen no; # don't couple langevin bath to hydrogens seed 82345 # Pressure control: no, constant volume useGroupPressure yes fixedAtomsForces off # PBC wrapAll on wrapWater on dcdUnitCell yes PME yes PMEGridSizeX 48 PMEGridSizeY 64 PMEGridSizeZ 45 rigidBonds all constraints off # Scripting minimize 200 reinitvels $temperature ;# run 10000000 ;# 10,000 ps run 10000000 ;# very short simulation for the practical