[gmx-users] question about energy minimization

Omer Markovitch omermar at gmail.com
Tue Sep 29 14:17:01 CEST 2009

Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed.

> I actually didnt realize this until i did a long simulation after which the
> trajectories of some of the atoms looked way out of the box dimensions. The
> co-ordinates of many atoms didnt lie in the box range. Although the output
> file contained the same box dimensions as I started with. Could someone help
> me in understanding what happened?
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