[gmx-users] pbc interference with g_dist

[Mark Abraham]

----- Original Message -----
From: Suman Chakrabarty <suman at sscu.iisc.ernet.in>
Date: Saturday, March 7, 2009 17:24
Subject: [gmx-users] pbc interference with g_dist
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi,
> 
> 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.

Use trjconv or editconf to change the size of the box, or use the -pbc no option of g_mindist.

Mark