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
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