[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Diez Fernandez, Amanda]

Hi all,
I am running a simulation and I find that the output coordinates of the simulation stored in “final_coordinates.gro” are distinctively different to any of the frames from “trajectory.gro” which I obtain from :

trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro

When I visualise final_coordinates.gro they look wrong, when I visualise trajectory.gro frame by frame it looks correct.

How can this be possible? Is it a common problem?

Thank you,

Amanda