[gmx-users] How to recover a corrupted .edr file

[Christopher Neale]

Thanks Peter. mdrun -rerun looks like a decent option. And thank you Mark for confirming the lack of skipping behavior.

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Peter Kroon <p.c.kroon at rug.nl>
Sent: 05 October 2017 04:38:03
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] How to recover a corrupted .edr file

Hi Christopher,


can you regenerate the edr file using -rerun and your salvaged
trajectory? That might be the easiest solution.


Peter


On 05-10-17 07:38, Christopher Neale wrote:
> Dear users:
>
>
> I recently experienced some corruption in a .xtc and a .edr file. Recovering the .xtc was pretty easy, I use gmx trjconv -b and -e to get the part before the corruption and the part after the corruption, which was itself a small chunk. This presumably works because trjconv actually skips to the -b time without reading through to get there.
>
>
> However, gmx eneconv seems to start reading always form the start of the .edr file. This is fine for a normal file, where it reads the initial frames through until the -b time and then starts writing to the output file. However, with a corrupted file, it causes problems because it hangs up on the corruption. To put it more planly, gmx trjconv fails with a corrupted .xtc but can recover a readable part beyond the corruption with a -b value just beyond the end of the corruption; this is not possible with my usage of gmx eneconv. I'm hoping that there is some alternative.
>
>
> Below is what I get with gmx eneconv from version 5.1.2. I als tried 2016.2 and got the same result. You can see that it lists the start time as "0" ps even though I sent it -b 379000. This is not a bug, since I tested with a non-corrupted file and gmx eneconv will respect the -b flag in what it writes out. It's just that eneconv can not seem to skip right to the -b point whereas trjconv can.
>
>
> GROMACS:      gmx eneconv, VERSION 5.1.2
> Executable:   /scratch/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
> Data prefix:  /scratch/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial
> Command line:
>   gmx eneconv -f 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr -b 379000 -o 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD_post_379000ps.edr
>
> Opened 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr as single precision energy file
> ^MReading energy frame      0 time    0.000         ^MReading energy frame      1 time    2.000
> Sorting disabled.
>
> Summary of files and start times used:
>
>           File                Start time
> -----------------------------------------
> 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr        0.000
>
> Opened 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr as single precision energy file
> ...
>
> ########
>
> Thank you,
> Chris.