crystal vibrates widely in NVT and NPT

Dear all,

I try to get a well equilibriated Al2O3 crystal at high temperature using comb3 potential. Timestep in my simulation is 0.2 fs. I started from 300K with fix nvt command:

fix 3 all nvt temp 300 300 0.02

run 500000

I found that the crystal began to vibrate from about 250000 step, but the vibration was not severe. Then I swithched to npt ensemble and heated the crystal from 300K to 600K with the following command:

fix 3 all npt temp 300 600 0.02 aniso 0.0 0.0 0.2

run 500000

During this process, the vibration became very obvious. What causes this vibration? Could you give me some suggestions on how to reduce the vibration?



If your time step is 0.2 fs there’s no way a damping time of 0.2 fs will work for the thermostat, let alone the barostat. The typical guideline is a damping time of 100 × time step size for the thermostat and 1000 × time step size for the barostat, though your mileage may vary.