[gmx-users] Measuring distance to the nearest image
anthony.nash at dpag.ox.ac.uk
Tue Dec 19 12:12:32 CET 2017
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.
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:
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?
On Mon, Dec 18, 2017, 5:23 PM Anthony Nash <anthony.nash at dpag.ox.ac.uk>
> 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.
> 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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