# Coulomb Crystal trapped by RF

# Steps
firststep 0
numsteps  100000

# System/topology
boundaryConditions Vacuum
cellManager        Cubic
cellsize           500000
exclude            none

# Positions
posfile examples/coulomb_309/309ca.pdb

# Velocities
temperature 0.001
#velfile 309ca.vel.xyz

# Molecular topology/atom definitions
psffile examples/coulomb_309/309ca.psf

# Force field
parfile examples/coulomb_309/309ca.par

# Random generator
seed 1234

# Modifications
#removeAngularMomentum 0
#removeLinearMomentum 0

#
# Output
#

# General/Screen output frequency
outputfreq 100

# PaulTrap relative output
#PAULFILE          309ca.out.paul           # Write PaulTrap output
#PAULLOWFILE       309ca.out.paul.low.xyz   # Write minimal positions and output
#PAULOutputFreq    10
#PAULCACHEFREQ     100                      # Cache 100 output lines before writing
#PAULOMEGA        2.6e-09                  # commented out to use values defined by force def.


# Trajectory position file
#DCDOutputFreq 100
#DCDFile       309ca.out.dcd

# Integration scheme
#Integrator {
#  level 0 PaulTrap {
#      timestep 1e+08      # [fs]
#      temperature 1e-28   # Temperature [K] if not defined by (t , time)
#      thermal 1e-7        # 1.0 => instantly, 0.0 => Leapfrog
#      scheme berendsen    # thermostat scheme
#
#      force Coulomb -algorithm NonbondedSimpleFull #-blocksize 64
#      # Multi-grid replacement for NonbondedSimpleFull
#      #    force Coulomb -algorithm MultiGrid -interpolation Hermite -kernel C2 
#      #          -s 500000 -levels 3 -h 250000 250000 250000  -order 6 -ratio 2

#      force PaulTrap -omegaR 2.6e-09 -omegaZ 2.6e-09
#  }
#}