[gmx-users] Measuring distance to the nearest image

[Anthony Nash]

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