[gmx-users] problems with some calculated trajectories

Martin Höfling martin.hoefling at lmu.de
Mon Jun 22 17:19:43 CEST 2009

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).


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