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

[SHAHEE ISLAM]

hi,
i am doing the contact between the all backbone beads within a protein
by using the below command.
gmx mdmat -f *.trr/xtc -s *.tpr -n index.ndx -mean dm.xpm -t 0.5
where -t is trunc distance.what value should i use for martini coarse
grained system because by changing -t value the plots are also
changes.
thanking you
shahee

On 12/19/18, Peter Kroon <p.c.kroon at rug.nl> wrote:
> Hi Shahee,
>
>
> what cutoff do you mean?
>
> You can find sample Martini MDP files here:
> http://cgmartini.nl/index.php/force-field-parameters/input-parameters.
>
> The normal VDW and coulomb cutoffs are 1.1 nm.
>
>
> Peter
>
> 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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