[gmx-users] Measuring distance to the nearest image

Anthony Nash anthony.nash at dpag.ox.ac.uk
Mon Dec 18 07:23:28 CET 2017

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.

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!

More information about the gromacs.org_gmx-users mailing list