[gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation

Dries Van Rompaey dries.vanrompaey at gmail.com
Wed Apr 13 15:55:08 CEST 2016


You can do this using built-in gromacs tools. You want to make a suitable
index group using gmx make_ndx, after which you can use gmx distance to
measure the distance between your groups.

On 13 Apr 2016 3:50 p.m., "Faulkner, Matthew" <M.Faulkner at liverpool.ac.uk>

> Hi all,
> Does anybody have a script, or reference where this has been done, for
> measuring distances between two residues in each time step of a simulation
> and exporting this data into a handy format like a text or csv file?
> I want to measure the distances over time between the nearest atoms of
> some residues that appear to have a conformation change but at the moment I
> only know how to do this manually.
> Regards,
> Matthew Faulkner.
> --
> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list