# 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              tpe_1ns
dcdfile                 tpe_1ns.dcd
restartname             tpe_1ns_restart

#fixed atom params
fixedAtoms  on


#set the fixed atom file param
#using X column reminds us the fix position is _not_ from this file.
#a value of 0 in this col means 'not fixed'

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                600
nonbondedFreq           1
PME                     yes
PMEGridSizeX            192 
PMEGridSizeY            144
PMEGridSizeZ            144
fullElectFrequency      4
stepspercycle           20

#PBC
xstFile                 tpe_1ns.xst 
xstFreq                 50 
wrapWater               on

# output
binaryoutput            yes
outputEnergies          25  
restartfreq             50 
dcdfreq                 50