[gmx-users] question about periodic boundary conditions

[Justin A. Lemkul]

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."

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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