ncl_pp_restart.in

#----------------------------------Initialization-----------------------------------

#log			pp_log_ncl.txt
#processors		* * * grid numa
#package		intel 0 omp 1
#dimension		3
#boundary		p f p

variable		t equal 100
variable		wI equal 1.0
variable		wO equal 0.02
variable		f equal 0.1
#variable		fI equal $f	#Percentage of hydrophilic area

#---------------------------------System Definition---------------------------------

#Simulation Box


read_restart		pp_restart_ncl_%.5000.bin


#---------------------------------Simulation Settings---------------------------------------

#force field

#pair_coeff	1 1 0.0103 3.405 8.5
#pair_coeff	2 2 0.41148 2.34 6.5
#pair_coeff	3 3 0.41148 2.34 6.5
#pair_coeff	2 3 0.41148 2.34 6.5
#pair_coeff	1 2 $(v_wI*0.06489) 2.872 11.9
#pair_coeff	1 3 $(v_wO*0.06489) 2.872 11.9

neighbor	0.35 bin
neigh_modify	delay 1

#groups

#group			ar type 1
#group			cuI type 2		#hydrophIllic
#group			cuO type 3		#hydrophObic
#group			cu union cuI cuO

#settings

#timestep	0.005

#Apply fix

fix		1 cu spring/self 4.3

shell		mkdir trajectory_ncl_$f
shell		cd trajectory_ncl_$f

fix		2 ar nvt temp $t $t $(10*dt)
fix		myfix cu nvt temp $t $t $(10*dt)
thermo		100
thermo_modify	lost ignore
#dump		1 all custom 100 tarj.all_atom.*.txt id type x y z
dump			1 all atom 100 traj_all_atom_*.txt
run		3000  

shell		cd ..
undump		1

compute	arTemp ar temp
compute	cuTemp cu temp 
thermo		1000
thermo_style	custom step temp c_arTemp c_cuTemp etotal press  
run		12000