VMD-L Mailing List

From: ruiyan (r-yan14_at_mails.tsinghua.edu.cn)
Date: Mon Jul 10 2017 - 17:34:40 CDT

Hello everyone,

I created a single single crystal in lammp. Because some atoms are very close to box boundaries and I can't avoid this, if I dump wrapped coordinates, it's hard to see whether atoms on the surface are still on the surface during a long simulation. So to better see whether the crystal is stable or not, I dumped unwrapped coordinates instead of wrapped coordinates. However, when I visualized lammps trajectory consisted of unwrapped coordinates in vmd, unlike wrapped coordinates, the crystal as a whole moves from one side to the other on the screen. I have two questions:

(1) Can I fix the crystal when I visualize a lammps trajectory file consisted of unwrapped coordinates and get a result like visualizing wrapped coordinates?

(2) I want to combine this crystal with another crystal from another simulation, using data files from these two simulations. There are no bonds in the two systems, just single atoms. Can I do this if some atoms on a surface of a crystal are slighly outside the box, especially if these atoms are on the surface which will be close to another crystal. Where will these atoms be, between the two crystal or somewhere else?

Thanks a lot and look forward to your response.

Rui