Dear all

I ran MD on a periodic cell with Forcite, and I want to get a trajectory map/ atomic density contour map from MD trajectory file.

I think trajectory map simply a map of the integrated atomic motions of chosen atomic types over the production phase of accumulated trajectories. In my case, I want to get trajecotry maps of atoms onto a grid in the a-b plane of a slice located along c  axis at position i and with thickness dzi. But I have no idea how to get atomic density map.

Does anyone have any idea how to draw those maps? What information in the trajectory files do I need?

Thank you!

Jingjing