[gmx-users] Measuring distance to the nearest image
anthony.nash at dpag.ox.ac.uk
Tue Dec 19 07:07:01 CET 2017
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.
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:
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!
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