I have a corrupt TRR file with a bad frame in the middle; I am wondering if I can remove just the bad frame to utilize all of my good data.
To obtain the corrupt TRR file, I first ran a simulation which died (at about 37.9ns) due to a disk quota restriction; this first simulation produced part1.trr. I restarted this simulation, and obtained part2.trr after the simulation finished successfully. I then used trjcat to concatenate these simulations (not aware that part1.trr ended on a corrupt frame), and the data were appended to part1.trr. Finally, to save disk space, I deleted part2.trr, confident that all 60ns of simulation data were in part1.trr. Not surprisingly, when I run any sort of analysis tool (including gmxcheck) it quits when it gets to the corrupt frame. Ideally, I would like to remove just the offending frame. I can use trjconv to extract the data up to the bad frame, but I can't use that utility to extract the good data past the bad frame, since it dies at the bad frame. For what its worth, part1.trr from the original run was about 2.1Gb, and part1 + part2 are about 3.4Gb. Any ideas how I could recover good data in a TRR file past a bad frame? Regards, Matt Wyczalkowski _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
