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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Peter Kroon <p.c.kr...@rug.nl> Sent: 05 October 2017 04:38:03 To: gromacs.org_gmx-users@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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
