# Rhodopsin model
variable N index on # Newton Setting
variable w index 10 # Warmup Timesteps
variable t index 520 # Main Run Timesteps
variable m index 1 # Main Run Timestep Multiplier
variable n index 0 # Use NUMA Mapping for Multi-Node
variable p index 0 # Use Power Measurement
variable c index 0 # 1 to use collectives for PPPM
variable d index 1 # 1 to use 'diff ad' for PPPM
variable x index 4
variable y index 2
variable z index 2
variable rr equal floor($t*$m)
variable root getenv LMP_ROOT
newton $N
if "$n > 0" then "processors * * * grid numa"
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
if "$c > 0" then "kspace_modify collective yes"
if "$d > 0" then "kspace_modify diff ad"
read_data ${root}/bench/data.rhodo
replicate $x $y $z
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt temp 300.0 300.0 100.0 &
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
if "$p > 0" then "run_style verlet/power"
if "$w > 0" then "run $w"
run ${rr}