[gmx-users] Measuring distance to the nearest image

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 19 12:02:12 CET 2017


This is exactly what two well chosen selections should produce, given a tpr
and the PBC option. What have you tried that didn't work as you expected?


On Mon, Dec 18, 2017, 5:23 PM Anthony Nash <anthony.nash at dpag.ox.ac.uk>

> Hi all,
> I am trying to measure the distance between the COM of two side chain
> functional groups across the periodic boundary to their nearest image
> rather than across the unit cell itself. I have tried several gromacs
> distance commands with no success and more at random as I trawl through the
> help and manual, so I won’t replicate those commands here.
> This link is a hand drawn image of what I am trying to do. I would like to
> measure how far apart the two large dots are across the periodic boundary.
> VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as it
> takes the measurement from within the unit cell.
> https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg
> If this involve a tcl script in VMD I would appreciate knowing how to code
> for an atom selection in a “Periodic” image rather than the “Self”.
> Loads of thanks!
> Anthony
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