# NAMD configuration file for energy minimisation of whole system # input coordinates ionized.pdb structure ionized.psf parameters par_all27_prot_lipid_na.inp paratypecharmm on # output set output emin outputname $output dcdfile ${output}.dcd xstFile ${output}.xst dcdfreq 100 xstFreq 100 binaryoutput yes binaryrestart yes outputEnergies 100 restartfreq 1000 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 2 stepspercycle 20 nonbondedFreq 2 fullElectFrequency 4 # Temperature control set temperature 298 temperature $temperature; # initial temperature # Langevin Dynamics langevin on; # do langevin dynamics langevinDamping 1; # damping coefficient (gamma) of 1/ps langevinTemp $temperature; # bath temperature langevinHydrogen no; # don't couple langevin bath to hydrogens seed 12345 # Pressure control langevinPiston on langevinPistonTarget 1.01325; # in bar -> 1.01325 bar = 1 atm langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp $temperature useFlexibleCell no useGroupPressure no fixedAtomsForces off # PBC # ** insert the correct values here ** cellBasisVector1 48.59 0 0 cellBasisVector2 0 65.276 0 cellBasisVector3 0 0 43.365 cellOrigin 0.5666550397872925 -4.781933307647705 0.3840275704860687 wrapAll on dcdUnitCell yes PME yes PMEGridSizeX 48 PMEGridSizeY 64 PMEGridSizeZ 45 # Scripting minimize 100