Greetings,
I intend to calculate the density of a system but unable to go further than 3 ps! It may be worth to note the cut-off distance is less than half of the simulation box length but this warning message appeared that maybe relevant to the problem: WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:667). Similar cases found having this warning message but unfortunately I couldn't figure out the solution and I'm not even sure that my problem is related to this message. Here is my input file and I highly appreciate any guidances help me run this simulation for more than 3 ps since I changed initial coordinates but didn't succeed.
#-------------Initialization----------------
dimension 3
boundary p p p
units real
atom_style full
timestep 1
#-------------Atom Definition---------------
pair_style lj/cut/coul/long 12.5
pair_modify tail yes
kspace_style ewald 1e-6
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0 dihedral yes
dihedral_style harmonic
improper_style cvff
read_data data.density
#-------------Settings/Run----------------------
neighbor 0.3 bin
neigh_modify every 2 delay 10 check yes
timestep 3
fix 1 all nve/limit 0.1
fix 2 all temp/rescale 100 298 298 0 1.0
variable density equal mass(all)*10/(6.0221417930*vol)
thermo 100
thermo_style custom v_density
run 1000
unfix 1
unfix 2
fix 1 all npt temp 298 298 100 iso 0.98692 0.98692 500 #298 K and 1 bar
print density
run 1000
Thank you in advance,
Negin