# NAMD Config file - autogenerated by NAMDgui plugin # Author: Jan Saam, saam@charite.de # input coordinates secondres.coor velocities secondres.vel structure ionized.psf parameters par_all27_prot_lipid_na.inp paratypecharmm on # output set output third outputname $output dcdfile ${output}.dcd xstFile ${output}.xst dcdfreq 5000 xstFreq 5000 #extendedSystem second.xsc binaryoutput no binaryrestart no outputEnergies 100 restartname thirdres restartfreq 1000 outputtiming 100 # mobile atom selection: # water or ion fixedAtoms on fixedAtomsFile third_fixed.pdb fixedAtomsForces on fixedAtomsCol O # Force field parameters exclude scaled1-4 1-4scaling 1 cutoff 10 switching On switchdist 8 pairlistdist 12 # Multiple timestepping firsttimestep 0 timestep 1 stepspercycle 20 nonbondedFreq 1 fullElectFrequency 1 #PME options PME yes PMEGridSizeX 60 PMEGridSizeY 72 PMEGridSizeZ 64 #PBC options cellBasisVector1 58 0 0 cellBasisVector2 0 70 0 cellBasisVector3 0 0 63 cellOrigin 0.7645 -5.9155 3.7545 # Temperature control set temperature 310 #temperature $temperature; # initial temperature useGroupPressure yes useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 100 langevinPistonDecay 50 langevinPistonTemp $temperature #temp constant langevin on; # do langevin dynamics langevinDamping 5; # damping coefficient (gamma) of 5/ps langevinTemp $temperature; # bath temperature langevinHydrogen no; # don't couple langevin bath to hydrogens seed 12345 # Scripting run 25000