[gmx-users] Measuring distance to the nearest image

[Mark Abraham]

Hi,

An example where the structure comes from a single frame would be a useful
thing to explore whether the code is working correctly. I don't think the
composition of the index groups should matter, but I can't see how the code
wouldn't work correctly.

Mark

On Tue, Dec 19, 2017, 10:12 PM Anthony Nash <anthony.nash at dpag.ox.ac.uk>
wrote:

> 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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