Hi Anthony,
Would it work if you take x/y/z components of the distance and subtract
ones extending the size of the box in the corresponding direction?
You will need to extract box size from the *.edr file (unless box is of
fixed size), further use flag -oxyz from gmx distance for xyz distance
components.
-Alexandr
On 19/12/2017 11:05, Peter Kroon wrote:
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.
Peter
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-boun...@maillist.sys.kth.se on behalf of
Anthony Nash" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of
anthony.n...@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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