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
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
