Hi,<br><br>Is there a way to quantitatively determine, from a trajectory file,
whether a molecule is interacting with a copy of itself in the adjacent
box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure file and viewed the
"periodic images to draw" under the Periodic tab of Graphical
Representations. <br>
<br>But I figure there's got to be an analytical way to do this, using g_dist or g_mindist? How the molecule is interacting (with its adjacent copy) is not the primary interest - I just want to know whether interactions among adjacent molecules are occurring.<br>
<br> Does anyone have any ideas?<br><br>Thanks,<br>Lili<br>