What I want to simulate is liquid crystal confined in a z-axis cylinder wall. The model just built by two kinds of atom. One is for the wall which will be fixed with fix freeze command. The other is for the liquid crystal. I am not sure about two parameters setting as bellow. Any comments will be appreciated.
boundary. We can set boundary with “s s p” or “p p p” but the box size of xy is much bigger than the cylinder diameter. In theoretic, will the two method give us similar result? Whether the former will save computation time?
fix npt groupid npt/asphere. I do not know whether the groupid here should be set as the whole system ( wall and liquid crystal) or just liquid crystal. As the introduction in manual, only the groups whose ID is set in fix command will be updated the velocity, position and other properties. Because I used fix freeze for wall, I think the position of wall should be not change or just scale with the whole box length in z axis. But there are some differences in the two dump file for the wall if I set the groupid for whole system and liquid crystal respectively. How should I set the group ID then?
Thanks in advance.