[gmx-users] Restart MD with overwritten CPT using TRR file in gromacs/2016.3

Abramyan, Tigran tigran at email.unc.edu
Fri Oct 27 22:24:23 CEST 2017


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:


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 trr

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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