[gmx-users] Measuring distance to the nearest image

[Anthony Nash]

Hi Mark,

As an example, from numerous attempts, I have tried: 

/usr/local/gromacs5.1.2/bin/gmx_d distance -pbc -b 10000 -f crosslinked_0_20.trr -s crosslinked_0_20.tpr -n index.ndx

which was throwing a value of around 8 nm, rather than the 2 nm I was expecting if it took a measurement from over the periodic boundary.

Unfortunately, I’ve left the necessary harddrive at home. I’’’ be more than happy to respond with a more comprehensive example along with output data in a few hours. 

Thanks
Anthony 
 

On 19/12/2017 11:02, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of mark.j.abraham at gmail.com> wrote:

    Hi
    
    This is exactly what two well chosen selections should produce, given a tpr
    and the PBC option. What have you tried that didn't work as you expected?
    
    Mark
    
    On Mon, Dec 18, 2017, 5:23 PM Anthony Nash <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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