title            = Equilibration 32 spc/e, 1 h3o+,  1.0 g/cm^3, 700K

# run parameters
nsteps          = 2          # for testing
step             = 0.0005      # = 0.5 fs (switch to 0.25 fs with 300K)
density          = 1.000       # g/cm^3, avg. density in constant pressure simulation at 300K.
temperature      = 700         # Kelvin

# set units
length-unit      = 1e-10          # => Ångstrøm
charge-unit      = 1.60217733e-19 # => Qe
mass-unit        = 1.6605402e-27  # => AMU

# temp control
const-temp       = 1        # nosé-hoover, takes over after scaling ended.
scale-end        = 125000   # 'shake well' for half of the equilib run.
scale-interval   = 20       # don't scale too often, let the system evolve.
const-pressure   = 0        # 
rtmass           = 100
ttmass           = 100

# restart settings
new-sys-spec     = 1        # initialize a fresh start.
lattice-start    = 0        # create a new restart.
text-mode-save   = 1        # save the results in text file, since we need 
#                            # the unit cell in the 'real' MD run.
# trajectory dump setting
begin-dump       = 10000000000
dump-interval    = 200
dump-level       = 1
ndumps           = 1000
backup-interval  = 200

# file names
save-file        = 32spce-h3op.sav
backup-file      = 32spce-h3op.bkp
temp-file        = 32spce-h3op.tmp 
dump-file        = 32spce-h3op-dump.%03d

# potentials
surface-dipole   = 0        # dangerous with ions. use only in unpolar systems.
strict-cutoff    = 1        # we want an isotropic system.
#cutoff           = 12.5     # let the md program guess
#subcell          = 2.0      # let the md program guess
#alpha            = 0.3      # let the md program guess
#k-cutoff         = 2.1      # let the md program guess

# rdf
nbins            = 1         # we use our own (and better) program to calc rdfs
begin-rdf        = 100000000 # we use our own (and better) program to calc rdfs

# screen output
page-width       = 132
page-length      = 500
reset-averages   = 0
begin-average    = 0
average-interval = 10000
roll-interval    = 1000
print-interval   = 1000
end

#################################################################
# Molecule geometries, masses and (partial) charges
#
# 32 SPC/E water in  Angstrom,    AMU,    Qe,  and   kJ Mol-1
spc/e  32
1   0.00000   0.00000   0.0641511  16  -0.8476   O
2  -0.81649   0.00000  -0.513209    1   0.4238   H
2   0.81649   0.00000  -0.513209    1   0.4238   H
# 1 h3o+ (potential derived from SPC/E)
h3op   1
3   0.00000   0.00000   0.000000   16  -0.2714   O
4   0.00000   1.00000   0.200000    1   0.4238   H
4   0.86603  -0.50000   0.200000    1   0.4238   H
4  -0.86603  -0.50000   0.200000    1   0.4238   H
end

#################################################################
# non bonded interactions (excl. coulomb)
lennard-jones
1  1   2.6008    3.166
1  3   2.6008    3.166
end