[gmx-users] Measuring distance to the nearest image

Peter Kroon p.c.kroon at rug.nl
Tue Dec 19 11:05:51 CET 2017

Hi Anthony,

I assume you've seen the -pbc flag of gmx distance; and IIRC there's
also some options for that in the selection syntax. I'm not sure that'll
do what you want though.

If you're going to make a script, have a look at the Python module
MDAnalysis, that has some nifty tools.

If you strictly use cubic boxes you can take the modulus of the distance
you measured --- but that'll bite you at some point in the future.


On 19-12-17 07:06, Anthony Nash wrote:
> Just wondering whether anyone has had any luck with a similar problem? If not, I’ll knock a script together and make it available. I was hoping not to reinvent the wheel if there was already a way. 
> Regards
> Anthony
> On 18/12/2017 06:23, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Anthony Nash" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of anthony.nash at dpag.ox.ac.uk> wrote:
>     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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