[gmx-users] g_covar warnings

João Henriques joao.henriques.32353 at gmail.com
Thu Mar 27 18:27:40 CET 2014

Hello everyone,

The documentation reads:

All structures are fitted to the structure in the structure file. When this
is not a run input file periodicity will not be taken into account.

This is rather cryptic, what does it mean in practice? No tpr, no party?
What if I use a properly centered and whole .gro file?

When ran with a .gro as the structure input file, I get two warnings. One
is related to the masses, which are non-existent in the .gro, but I don't
need them anyway. The second warning is honestly confusing me even more.

WARNING: If there are molecules in the input trajectory file
         that are broken across periodic boundaries, they
         cannot be made whole (or treated as whole) without
         you providing a run input file.

The documentation points out to the structure input file and now it's the
trajectory? What's going on? Do I also need to make each frame whole in the
input .xtc? Can someone elaborate on this?

Thank you in advance,
Best regards,
João Henriques

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