# NAMD torque 1 rev/ns f1 atpase # Barry I. 2001-Apr-5 # input coordinates f1wations_xplor.pdb structure f1wations_xplor.psf BinCoordinates f1wations-pme-nve-200ps.coor BinVelocities f1wations-pme-nve-200ps.vel ExtendedSystem f1wations-pme-nve-200ps.xsc parameters IONS27_par_all22_prot_na.inp paratypecharmm on outputname /usr/tmp/f1atpase #fixed atom params fixedAtoms on fixedAtomsFile f1_pme_fixed_3.pdb fixedAtomsCol X # force field parameters exclude scaled1-4 1-4scaling 1.0 cutoff 11 switching On switchdist 9 pairlistdist 13 # integrator params timestep 1.0 numsteps 500 nonbondedFreq 1 PME yes PMEGridSizeX 192 PMEGridSizeY 144 PMEGridSizeZ 144 fullElectFrequency 4 stepspercycle 20 # output outputEnergies 1 outputTiming 20