[gmx-users] Restart MD with overwritten CPT using TRR file in gromacs/2016.3
mark.j.abraham at gmail.com
Sat Oct 28 03:16:19 CEST 2017
There's always two cpt files on disk so this should never be needed, even
if the parallel file system does the usual lie of telling mdrun that it has
flushed to disk when it may or may not have done so...
On Fri, 27 Oct 2017 22:24 Abramyan, Tigran <tigran at email.unc.edu> wrote:
> Because one of my gromacs/2016.3 jobs accidentally crashed and got
> restarted and overwrote the CPT file, I am now attempting to continue a
> simulation using the TRR file. For this I ran the command 'gmx convert-tpr
> -s md.tpr -f md.trr -o md_next.tpr', so that I could use 'md_next.tpr' file
> to restart the simulation, but obtain the following error:
> READING COORDS, VELS AND BOX FROM TRAJECTORY md.trr...
> trr version: GMX_trn_file (single precision)
> Read trr frame 7519: step 150380000 time 300760.000
> Program: gmx convert-tpr, version 2016.3
> Source file: src/gromacs/fileio/trrio.cpp (line 114)
> Fatal error:
> Failed to find GROMACS magic number in trr frame header, so this is not a
> The same command (only replace 'gmx convert' to older version 'tpbconv')
> works fine in gromacs/4.6.3.
> Additionally, I was wondering, why doesn't gromacs automatically 'hash'
> backup the CPT file along with the other files? Does that mean that CPT
> file probably has info (e.g., velocities) from the previous run, which
> didn't get overwritten?
> Please help.
> Tigran M. Abramyan, Ph.D.
> Postdoctoral Fellow, Computational Biophysics & Molecular Design
> Center for Integrative Chemical Biology and Drug Discovery
> Eshelman School of Pharmacy
> The University of North Carolina at Chapel Hill
> Chapel Hill, NC 27599-7363
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