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

[Dries Van Rompaey]

Hi,

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.

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

> 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.
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