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

Peter Kroon p.c.kroon at rug.nl
Wed Dec 19 10:44:39 CET 2018

Hi Shahee,

what cutoff do you mean?

You can find sample Martini MDP files here:

The normal VDW and coulomb cutoffs are 1.1 nm.


On 19-12-18 09:30, SHAHEE ISLAM wrote:
> 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
> shahee
> 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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