Problem with extremely small time step

Respected sir/madam,
I’m running stress simulations on single layer graphene sheet. I’m getting an error of atoms lost when i runned with 5fs time step. I decreased the time step till solve the error i.e 0.0005fs which is ridiculously small.
Here is my input script please give me some suggestions to control potential energy and to run with 5fs time step that should not effect stress calculations.

units metal
atom_style atomic

boundary f p f
newton on
processors 1 1 1

dimension 3
read_data Sheet_Input.txt
mass 1 12.01
pair_style airebo 2.0
pair_coeff * * CH.airebo C

neighbor 2.0 bin
neigh_modify delay 3

timestep 0.0000001
fix 1 all npt temp 300.0 300.0 0.05 y 0 0 0.5
thermo 2000
compute 1 all stress/atom NULL
compute 2 all pe/atom pair bond
compute 3 all reduce sum c_1[1] c_1[2] c_1[3]
thermo_style custom step temp pe ke etotal press lx ly pxx pyy c_3[1] c_3[2] c_3[3]
run 600000
unfix 1
fix 1 all nvt temp 300 300 0.05
fix 2 all ave/atom 1 1000 1000 c_1[1] c_1[2] c_1[3] c_2 fx fy fz
dump 1 all custom 1000 dump.new.* id type x y z vx vy vz c_1[1] c_1[2] c_1[3] c_2 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7]
dump 2 all xyz 10000 dump.graphene.*.xyz
variable srate equal 1.0e9
variable srate1 equal “v_srate/1.0e12”
fix 3 all deform 1 y erate ${srate1} units box remap x
run 6000000

Thanks & Regards,
Venkata Pavan Kumar. Miriyala
[email protected]…24…,
contact number: +91-9032307746

Respected sir/madam,
                 I'm running stress simulations on single layer graphene
sheet. I'm getting an error of atoms lost when i runned with 5fs time step.
I decreased the time step till solve the error i.e 0.0005fs which is
ridiculously small.

perhaps it is not the timestep directly that causes the problem, but
your initial geometry is incorrect and has atoms in close contact or
your system is too close to the box boundaries (have you tried "m"
instead of "f"?). have you visualized your system and seen anything
unusual?

axel.