|Date:||Tue, 24 Apr 2018 22:51:48 +0800 (GMT+08:00)|
I recently simulated crosslinked epoxy resins. I encountered problem of missing bonded atoms for quite a while. When using LJ potential (dreiding forcefield), everything is fine, but when switching to X6 potential (for relaxation after the crosslinking process using LJ potential), the run crash all the time at a certain step, although I have adjusted the timesteps,neighbouring list and so on.
I asked a researcher who has done relevant simulation. He told me that he also has missing atoms when there is atom type of H__A (in dreiding, H__A is Hydrogen possible of forming h bond). And then he changed H__A to H_(normal hydrogen), the problem was solved. The difference between H__A and H_ is that the vdw interaction with a H__A is several orders lower than with H_. I followed this way and no missing atoms were found anymore, and the simulation can keep going. One question is that is it a really correct way to change H__A to be H_ ? Will the results be not realistic ? Then I tried to use another way to constrain H__A by fix shake and rattle, using
fix 101 all shake/rattle 0.0001 20 0 t 7 # the type of H__A is 7 in my data file
but I still encounter missing atoms using either shake or rattle. Could anyone help to see if I have provided an effective constraint?
Another question is more general. I understand that X6 potential provide much softer cores compared with LJ. But why soft cores can cause bad dynamics? And since these two potentials are quite different, leading to much different densities for example, how can we judge which one is more realistic and which one is not ?