On Aug 11, 2013, at 2:12 PM, Justin Lemkul wrote: > > > On 8/11/13 9:16 AM, Joshua Adelman wrote: >> I recently had a simulation crash where my .trr and .xtc files extend beyond >> the last checkpoint time (I'm using 4.6.3). Explicitly something like >> run_002.trr was written after state.cpt. I was wondering if there was a >> recommended protocol for truncating run_002.trr such that when I restart >> from the checkpoint, starting the next trajectory file in the series, >> run_003.trr will be continuous with the previous one? This is important in >> terms of going back and treating the series of trajectory files as >> continuous for analysis purposes. >> >> My preliminary thought is to get the timestamp, T, of the state.cpt file >> using gmxcheck, and then do `trjconv -f run_002.trr -trunc T`. This seems to >> work (although I need to check if the coordinates in the truncated file >> match with the state.cpt file). When I try the same thing with my .xtc file, >> I get an error message: >> >> Fatal error: >> run_002.xtc is not a trajectory file, exiting >> >> This seems strange since running gmxcheck on the xtc file doesn't report any >> issues. >> >> Any suggestions on the proper way to clean up the files or the error message >> would be appreciated. >> > > There is no need to truncate anything. If you're concatenating later with > trjcat, they will be stitched together properly with frames from the second > trajectory overwriting the frames in the first (i.e. the stretch in > run_002.trr that is "past" the checkpoint will be re-calculated in > run_003.trr and incorporated seamlessly). The trjcat documentation alludes > to this behavior. > > -Justin > >
Hi Justin, Thanks for your reply. Unfortunately, I was not intending to concatenate the files, especially in light of the total continuous trajectory taking up a large amount of disk space. I guess I could just use trjcat on any xtc file where there was a crash with the subsequent one in the series and use the output instead, but I'd rather just remove the frames past the checkpoint so that I can process all of the files without any special checking for this case. Also, I was looking at the source for gmx_trjconv.c and it looks like the truncation routine doesn't accept xtc files (although I could be wrong since I haven't spent much time looking at Gromac's internals): https://github.com/gromacs/gromacs/blob/d67173b36b78840466e691a4a6657d2b8fdb1c84/src/gromacs/gmxana/gmx_trjconv.c#L463 This does not appear to be documented outside of looking at the source. This seems particularly confusing because trjconv does take xtc files and the error message is a little misleading since xtc is a trajectory file, but just not one of the formats that is allowed with trunc. Alternatively, I think I could use the `-e` flag to specify the last frame that I want corresponding to the checkpoint and write to a new file rather than truncating in-place. Does that sound reasonable? Thanks again for your help. Josh -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
