[gmx-users] Regarding the atomic contact map in gromacs

[Mijiddorj B]

> Message: 1
> Date: Thu, 21 Nov 2019 08:35:57 +0000 (UTC)
> From: Dorj Bat <batdorj230 at yahoo.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Regarding the atomic contact map in gromacs
> Message-ID: <1668926834.3378277.1574325357108 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
> My simulation system contains pentamer of a short peptide. I would like to
> analysis the atomic contact map. However, gmx mdmat can give us the contact
> map of residues, not the atomic map. Is it possible to get this contact
> information. Please suggest me possible internal or external tools.
>
> Bat
>
> gmx mindist counts the contacts within a certain range, and you can
calculate all contacts and every possible contact number for each pair.
Then, normalize the pair contact number in order to get the probabilistic
values of the pairs. Finally, you can get the matrix, and show the figure
plot of gnuplot.

Mijiddorj