Problem in restrain

Dear users,
I am doing MD simulation of ZnO. But after NVT equilibration the surface is distorted. I am attaching the screenshot. So I think I have to restrain the bonds and angles. But I dont know how to restrain these. I have tried but got error. My input script is below:

REAX potential for ZnOH2 system

units real
atom_style charge

#atom_modify map yes
#atom_modify map hash sort 10000 2.0
#atom_modify first colloid
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0

pair_style reax/c NULL
pair_coeff * * ffield.reax.ZnOH O Zn

thermo 100
thermo_style custom step temp pe press vol lx density
dump 2 all xyz 100
dump_modify 2 element O Zn

fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
minimize 1.0e-10 1.0e-10 10000 10000
run 1000

#fix 1 all nve
#fix 3 all temp/berendsen 500.0 500.0 100.0
#reset_timestep 0
#timestep 0.25
#run 1000

#fix 1 all nvt temp 300 300 100
#reset_timestep 0
#timestep 0.25
#run 10000
#unfix 1

fix 1 all npt temp 300 300 100 iso 0 0 1000
reset_timestep 0
run 10000
unfix 1

print “All done!”

Please help me.

Screenshot from 2019-04-26 15-43-01.png

Screenshot from 2019-04-26 15-42-54.png

Restraining bonds and angles are just fixing the symptom not the problem which is a very bad idea. Your structure seems like a single sheet of ZnO – is that really your intention?


Agreed. The VMD figures suggest that the in-plane box size might
be too small, causing large corrugations.
You can either try using NPT to relax the box or, if it does not work
(NPT usually has problems with soft low-dimensional materials),
change the box size by hand and check the resulting in-plane stress.
A zero-stress (if this is what you intended)
state can be obtained by try and error.


Thank you for your clarification. This is a zno single sheet and I want to see the interactions between this single sheet and water. So is this distorted surface can cause any problem? Or I can continue with the same single sheet? The box size is about 1x60x60. Do I have to increase the box size?
Please help me.


It depends on your own requirement. If you require (or think, or hope) the sheet has zero in-plane stress, you need to achieve it in some way. I mentioned two ways in my last email: using NPT or try-and-error. As long as the stress is correct, whatever configuration you will get just reflects the properties of the potential (force field) you use.