Dear friends,
I am working on modelling of polymer. Generally in my simulation I use special_bonds amber. However, since I need to use the fix bond/break option I had to change the special bonds to fene. Using the fene option it does not just work properly. That is to say, when I run the system it just crashes. I checked the results in few steps using VMD and I saw some atoms are shooting out of system.
Previously I ran similar structure with the same potentials but this time I do not know what is exactly the problem.
Part of my input file is given below.
Any suggestion to solve the problem would be highly appreciated.
Kourosh,
Are you trying to use fix bond/break on an all-atom model of
a polymer, e.g. an AMBER model? Does it have angles/dihedrals?
If so, it won't work. As the fix bond/break doc page states:
When a bond is broken, you might wish to turn off angle and dihedral
interactions that include that bond. However, LAMMPS does not check
for these angles and dihedrals, even if your simulation defines an
angle_style or dihedral_style.
If you just have bonds, the doc page also states:
IMPORTANT NOTE: Breaking a bond typically alters the energy of a
system. You should be careful not to choose bond breaking criteria
that induce a dramatic change in energy. For example, if you define a
very stiff harmonic bond and break it when 2 atoms are separated by a
distance far from the equilibribum bond length, then the 2 atoms will
be dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds.
This can lead to hi-energy atoms and what you observed in VMD.
Steve