############### Gaussian Potential Test ###############
units           real
atom_style      full
boundary        p p p

bond_style      gaussian
angle_style     harmonic
dihedral_style  harmonic
pair_style      lj/gromacs 12.0 15.0
pair_modify     mix arithmetic 

read_data       Two_beads.data

bond_coeff      1 300 1 0.0128 0.375 3.0  # New gaussian bond potential
angle_coeff     1 50.0	92.1
dihedral_coeff  1 0.111111	1	3
pair_coeff      1 1 0.0957 3.03315

neighbor        2.5 bin
neigh_modify    delay 5

variable 		TI equal 1000     # Initial Temperature
variable 		TF equal 300      # Final Temperature

timestep        0.5

######################################################
thermo          10000
thermo_style	custom step temp pxx pyy pzz ebond eangle edihed eimp epair ecoul evdwl pe ke etotal lx ly lz vol density

#variable        den equal "density"
#fix             65 all print 1000 "${den}" file density.txt

dump            tra all custom 25000 All.lammpstrj id type x y z 
dump            5 all dcd 50000 relax_wrap-1.dcd
dump            55 all dcd 50000 relax_unwrap-1.dcd
dump_modify     55 unwrap yes

#####     energy minimization     #####
velocity        all create ${TI} 54355 rot yes
velocity 	    all zero linear
minimize 	    1.0e-12 1.0e-12 50000 50000

reset_timestep  0

#####     NPT annealing     #####
fix             50 all npt  temp ${TI} ${TI} 50  iso 1 800 500
run             250000  
unfix           50

fix             51 all npt  temp ${TI} ${TI} 50  iso 800 800 500
run             250000  
unfix           51

fix     	    52 all npt  temp ${TI} ${TI} 50  iso 800 1 500
run             250000 
unfix           52

fix     	    53 all npt  temp ${TI} ${TI} 50  iso 1 800 500
run             250000 
unfix           53

fix             54 all npt  temp ${TI} ${TI} 50  iso 800 800 500
run             250000  
unfix           54

write_data      Relax_Anneal-1.data
write_restart   Relax_Anneal-1.rest

fix     	    55 all npt  temp ${TI} ${TI} 50  iso 800 100 500
run             250000 
unfix           55

fix     	    56 all npt  temp ${TI} 750 50  iso 100 1 500
run             250000 
unfix           56

fix     	    57 all npt  temp 750 500 50  iso 1 1 500
run             250000 
unfix           57

fix     	    58 all npt  temp 500 ${TF} 50  iso 1 1 500
run             1000000
unfix           58

fix     	    59 all npt  temp ${TF} ${TF} 50  iso 1 1 500
run             2000000
unfix           59

write_data      Equil-1.data
write_restart   Equil-1.rest

undump          5
undump          55

#####     Probability Distribution Sampling    #####
dump            5 all dcd 1000 wrap-1.dcd
dump            55 all dcd 1000 unwrap-1.dcd
dump_modify     55 unwrap yes

fix     	    57 all npt  temp ${TF} ${TF} 50  iso 1 1 500
run             2000000
unfix           57

print "ALL DONE"