[gmx-users] pbc interference with g_dist

Suman Chakrabarty suman at sscu.iisc.ernet.in
Sat Mar 7 07:23:58 CET 2009


after spending a long time with a seemingly wrong result with g_dist,
I discovered that g_dist actually uses pbc and nearest image
convention to calculate the distance.

As a result, the end-to-end distance of my polymer chain is calculated
as 1.5 nm, while actually it should be 12.44 nm (box length = 13.9422
nm). Since I am interested in the end-to-end distance of the single
polymer chain irrespective of the position of the two ends, I would
like to know what would be the best way to go about it.

I hope I could explain my problem.

Thanks and regards,

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