GROMACS Users emailing list more appropriate for this question.

You can used editconf to translate, rotate coordinates around.  So
move the 2nd one around, then copy / paste the coordinates into the
1st coordinate file, making sure adjust the atom number count and
maintain the correct header/footer format.  Another option is loading
into vmd and manually moving the molecules around, then saving the
coordinates.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 13 February 2018 at 10:41, Armin Solemanifar
<armin.solemani...@gmail.com> wrote:
> Dear Gromacs users,
>
> I'm trying to put two peptides inside the simulation box and have the
> ability to rotate them to face each other in a particular way before
> starting the simulation. I only know how to put them randomly in the
> simulation box.
>
> My second question is how to put them in a certain distance from each other
> in the beginning as well.
>
> Cheers,
> Armin
>
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