[gmx-users] orientation of helical peptide

[Louic Vermeer]

Dilraj Lama wrote:
> hello gmx-users,
>                 I have two helical peptide of 16 residues each.I want to orient these peptides
> parallel to each other in one case and perpendicular to one another in another.How
> can I do this using Gromacs?
> 
> Please suggest.
> 
> Thank you.

I would suggest to use a visualisation program like molmol or VMD to do 
the job. You could just drag & drop the helices roughly the way you want 
them.
It might however be "more scientific" to write a script to do the job, 
but it could be that you don't need that kind of accuracy.

Have fun!
Louic