[gmx-users] contact analysis between the all backbone of same protein

SHAHEE ISLAM islamshahee at gmail.com
Wed Dec 19 09:30:35 CET 2018

thank you so much for your reply.
I have done according your instruction.Can you please tell me what
should best cut off for martini coarse grained force field.
 thanking you

On 12/18/18, soumadwip ghosh <soumadwipghosh at gmail.com> wrote:
> Hi,
> You can obtain the backbone atom contacts in the same protein using the gmx
> mdmat command.
> gmx mdmat -f *.trr/xtc -s *.tpr -n index.ndx -mean dm.xpm -t 0.5 (the -t
> option is because you want the protein contacts within 0.5 nm I guess).
> When prompted, select the correct group from index file. It will ask you
> for the group only once.
> Then post process the .xpm file into an eps file using,
> gmx xpm2ps -f dm.xpm -o dm.eps -rainbow red
> One can view the .eps file in eps viewer and convert it into a .png or
> .tiff file.
> Best of luck!
> Soumadwip Ghosh
> Post Doctoral Research Associate
> Dept of Molecular Imaging & Therapy
> City of Hope National Medical Center
> Duarte, CA - 91010
> United States
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