[gmx-users] Confuse about trjconv tool

[Caizk]

Dear users,

I was following Justin's tutorial and in the analysis step trjconv was used to account for any periodicity in the system and then analyses were conducted with the so-called "corrected" trajectory file.

The first question is: does it means that particles might diffuse though one side of the box and doesn't get into the box from the opposite side? 

If not, why does trjconv have to be used? If so, why could't gromacs maintain the periodicity of all particles' coordinates in the production MD?

Finally, Is it necessary to use trjconv to currect the trajectory file every time before you conduct any analysis?


Please correct me if something is wrong. Your reply will be highly appreciated.

Wishes,
Zhikun