Hey Bernhard, here some thoughts of mine:
In principle, vmd should be able to read the trajectories if pdb2gmx
tells you that the trajectory is ok. If this is not the case, you can
use gmx_rescue64 to extract the undamaged parts.
Reasons for damaged trajectories, even when gromacs runs through fine...
... for me - filesystem issues were causing this. In particular this
happened for me with NFS shares and on Lustre filesystems. My NFS
problems got solved with an upgrade of the NFS packages on our
machines (at least 1 1/2 yrs ago).
Best
Martin
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