bad dynamics of lj+shifted truncated lj interaction for bead spring chain


yesterday I posted these input files. the problem was atoms were blown out of simulation box and stuck there. I added special bonds but didn’t help. cut off is also large enough that two lj interacting atoms can see each other. the point is this works with very small time step (0.000005) and not ridiculously large lj epsilon. to the best of my knowledge that doesn’t matter how large is lj epsilon.

this might be very stupid mistake, I very much appreciate if any one gives this any thought and let me know about your experience.



in_strain.dat (1.02 KB)

data_long.dat (644 KB)

You would be better off debugging this
yourself, since you know your model. You can

monitor the thermo output every timestep, and dump
positions and forces to a file every timestep. So you
can see yourself if there are large forces leading to
bad dynamics and a bad model. 99 times out
of 100 this is due to bad inputs, and again, you
are the best person to figure it out.