log eq4.log append
units real
atom_style full
boundary p p p

pair_style lj/charmm/coul/long 8.0 12.0
kspace_style pppm 1e-6
dielectric 1.000000
bond_style harmonic
angle_style harmonic
dihedral_style fourier
improper_style cvff
special_bonds amber
pair_modify mix arithmetic
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
read_data eq4.data

thermo_style custom step time temp press enthalpy etotal ke pe ebond eangle edihed eimp evdwl ecoul elong etail vol lx ly lz density pxx pyy pzz pxy pxz pyz
thermo_modify flush yes
thermo 1000

dump dump0 all custom 1000 eq4.dump id type mol x y z ix iy iz vx vy vz
dump xtc0 all xtc 1000 eq4.xtc
dump_modify xtc0 unwrap yes
restart 10000 radon_md_1.rst radon_md_2.rst

timestep 1.000000
compute cmol1 all chunk/atom molecule nchunk once limit 0 ids once compress no

# rg
compute gyr1 all gyration/chunk cmol1
fix rg1 all ave/time 1 1000 1000 c_gyr1 file rg4.profile mode vector

# msd
compute msd1 all msd com yes average no
fix msd1 all ave/time 1 1000 1000 c_msd1[4] mode scalar
variable msd equal f_msd1
thermo_style custom step time temp press enthalpy etotal ke pe ebond eangle edihed eimp evdwl ecoul elong etail vol lx ly lz density pxx pyy pzz pxy pxz pyz v_msd
thermo_modify flush yes
thermo 1000
fix shake1 all shake 1e-4 1000 0 m 1.0

# npt
fix md1 all npt temp 100.000000 100.000000 100.000000 iso 1.000000 1.000000 1000.000000 nreset 1000 

run 5000000
unfix md1
uncompute cmol1
unfix rg1
uncompute gyr1
unfix msd1
uncompute msd1
unfix shake1

write_dump all custom eq4_last.dump id x y z xu yu zu vx vy vz fx fy fz modify sort id
write_data eq4_last.data
quit