[gmx-users] how could have integrated structure after sa.

[Mark Abraham]

Homa Azizian wrote:
> Hi
> 
> 1- Is it possible to change the pbc condition from xyz(default) to 
> no(vacume)
> after finishing the annealing, in order to reach an integrated sturcture 
> instead of wraped one?
> 2- What command should I execute? is fixed by trjconv?  
> 3-It is probably a simple question, in MD we have also PBC set to xyz but 
> the final structure is not wraped, what is the resean?

For both this query and your next one, I think the information here 
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions will help 
you understand that things are probably fine, and that you may need 
suitable application of trjconv to make them suit your visual requirements.

Mark