Humic Substances Simulation


I’m trying to simulate a system containing water molecules and humic substances (humic and fulvic acid), but when I run the simulation, the bonds present in the acids are broken. I’m using a reactive force field and a temperature of 300K for 1ns, could someone tell me how to make the acid bonds not break at this temperature? The script referring to system optimization and balance is presented below:

thermo 1000
thermo_style custom step temp etotal ke pe press lx ly lz

#dump min all custom 1000 minimization_nsimu.lammpstrj id type mass x y z q
#minimize 1.0e-5 1.0e-6 100000 1000000
#min_style cg ## minimization (using CG method)
#undump min

group humic_acids type 1 2 5 6 8 9 11 12 13
group water type 3 4

#fix 2 all wall/lj126 zlo EDGE 0.07 3.550053 10.0
#fix 3 all wall/reflect zhi EDGE

velocity humic_acids create 300 312839 rot yes mom yes
velocity water create 300 312839 rot yes mom yes

#fix 2 water npt temp 300 300 10 iso 1.0 1.0 100 ## units real gives temp in kelvin and pressure in atm
fix 2 water nvt temp 300 300 10 ## units real gives temp in kelvin and pressure in atm

#fix frozen particle move linear 0.0 0.0 0.0

dump 1 all custom 1000 nvt_mdz_nsimu.lammpstrj id type mass x y z q
run 1000000

Best regards,

What reactive force field? It’s not shown in your script.
Is it parameterized for this material and model?


Yes, it is parameterized for both.

You didn’t answer what pair style. If it is ReaxFF, I suggest you ask
the folks who parameterized ReaxFF for that system and ask them if
it suitable for your simulation model. The LAMMPS simulation is doing what
ReaxFF induces it to do. If bonds want to break with that parameterization, they will break.