[gmx-users] trjconv center on protein

[Tomek Wlodarski]

Hi all!

I have a trajectory of simulation (protein in box of water) and I
would like to have all the time protein in the center of the water
box, becasue protein is drifting to the edge during simulation and I
am calculating some properties of water arround the protein.
I was playing with trjconv and -pbc and -center options and I menage
to do what I wanted, however there was something bizarre for me or
maybe I do not fully understand how this centering works....
I noticed that the same water molecule traverse different distance
between the same frames of simulation in the original than in
converted trajectory...
Why and how it is possible?
Thank you for any suggestions and help!
Best!

tomek