[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

Ioannis Beis Ioannis.Beis at oulu.fi
Thu Apr 25 20:00:35 CEST 2013

Dear Gromacs users,

I have some corrupted frames in different trajectories. gmxcheck with .trr trajectories gives extraordinary positions or velocities and with .xtc trajectories gives rise to the magic number error. I am aware of the program gmx_rescue kindly offered to us by its developers. However, this program can only work with .xtc files. It is possible to rescue .trr files when there is a maximum of one corrupted frame by checking the size of healthy frames, chopping the parts of the trajectory before and after, using e.g. programs head and tail with the corresponding integer multiples of one healthy frame in bytes and stitching them together. However, when there is two or more corrupted frames in different locations, although it is not hard to spot the exact locations, it is no longer possible to remove the problematic frames size-wise (or at least it is less likely to succeed than winning the lottery) , since the size of each corrupted frame is non-standard. Is there any corresponding software to gmx_rescue that can be used with .trr files? Is there any other recent program or any other way of coping with the problem? I did not post any details of my systems or the specific error messages I get because I believe my question is clear.

Thank you in advance!


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