[gmx-users] question about periodic boundary conditions

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 20 22:22:17 CEST 2010

rainy908 at yahoo.com wrote:
> Hi,
> 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. 
> 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.

 From g_mindist -h:

"With option -pi the minimum distance of a group to its periodic image is
plotted. This is useful for checking if a protein has seen its periodic image
during a simulation. Only one shift in each direction is considered, giving a
total of 26 shifts. It also plots the maximum distance within the group and
the lengths of the three box vectors."


> Does anyone have any ideas?
> Thanks,
> Lili


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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