# LAMMPS Configuration  file

units 		real
atom_style 	full
dimension 	3
boundary 	p p p

# Force field

pair_style 	lj/cut/coul/long 9.0 9.0			
pair_modify	mix geometric
# pair_modify	table 0
bond_style 	hybrid morse harmonic	# Energy for bond stretch
angle_style 	harmonic					# Energy for angle bend

read_data  	input.data			# Input file coordinate parameters

kspace_style 	pppm 1.0e-5					# Electrostatic interactions above cutoff 

# User-defined groups

group water type 15 16
group lower type 1 2 3 4 6  
group upper type 8 9 10 11 13
group lowerslabh type 5 7
group upperslabh type 12 14
group slabs union lower upper
group lwh union lower lowerslabh
group uwh union upper upperslabh

# neighbor_list

neighbor 	 2 bin
neigh_modify	 every 1 delay 0 check yes

fix 	1 water shake 0.0001 10 0 b 3 a 3

fix		2 all nvt temp 293.15 293.15 20

fix 3 slabs spring/self 200.0

velocity	all create 293.15 345678 dist gaussian

timestep 0.1

# equilibration run
thermo 1000
thermo_style	custom step atoms temp press pe ke epair pxx pyy pzz vol density	# where vol = sim box volume
thermo_modify lost warn
run 10000
# unfix 1
unfix 2	

reset_timestep 0
timestep 1.0

fix		2 all nvt temp 293.15 293.15 100 

# EQUILIBRATION 10ns:
thermo 		1000
thermo_style	custom step atoms temp press pe ke pxx pyy pzz 		
thermo_modify lost warn
run 		150000					# Number of timesteps temporary change from 10000000

unfix 2
unfix 3

fix 2 lwh nvt temp 293.15 293.15 100
fix 3 lower spring/self 200.0

fix 4 water nvt temp 293.15 293.15 100

fix 5 upper rigid/nvt single temp 293.15 293.15 100

fix 6 upperslabh nvt temp 293.15 293.15 100

# PULLING:

fix 7 all colvars PMF-Olivera.colvars 
dump		1 all custom 10000 output.data id mol type q x y z
dump_modify     1 sort id

restart         100000 restartmelt.restart
run 		2300000					# Number of timesteps: targetNumSteps×(targetNumStages+ 1)