[gmx-users] restart nvt run

Justin Lemkul jalemkul at vt.edu
Sun Feb 4 14:35:26 CET 2018

On 2/4/18 5:26 AM, farial tavakoli wrote:
> Dear GMX users
> I ran nvt simulation on my complex using gromacs2016.4. But faced to this error:File input/output error:
> Cannot read/write checkpoint; corrupt file, or maybe you are out of disk
> space?
> so I deleted some files to make free space and then issued this command to restart the simulationgmx mdrun -s nvt.tpr -cpi nvt.cpt but faced to this error:
> Output file appending has been requested,
> but some output files listed in the checkpoint file nvt.cpt
> are not present or not named as the output files by the current program:
> Expect output files present:
> Expected output files not present or named differently:
>    nvt.log
>    nvt.trr
>    nvt.edr
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016.4
> Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
> "Fatal error:
> File appending requested, but 3 of the 3 output files are not present or are
> named differently. For safety reasons, GROMACS-2016 and later only allows file
> appending to be used when all files have the same names as they had in the
> original run. Checkpointing is merely intended for plain continuation of runs.
> For safety reasons you must specify all file names (e.g. with -deffnm), and
> all these files must match the names used in the run prior to checkpointing
> since we will append to them by default. If you used -deffnm and the files
> listed above as not present are in fact present, try explicitly specifying
> them in respective mdrun options. If the files are not available, you can add
> the -noappend flag to mdrun and write separate new parts. For mere
> concatenation of files, you should use the gmx trjcat tool instead."
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>   I renamed my files in this way:nvt.log to md.lognvt.edr to ener.edrnvt.trr to traj.trrnvt.cpt to state.cptnvt.tpr to topol.tpr
> but faced to the "fatal error" again. is there any one can help me? I dont want to use -noappend flag.

Don't rename the files; that is the exact opposite of what you want to 
do. The error message is quite clear. The .cpt file expects files with 
certain names to be present. If you've removed, moved, or renamed them, 
appending will fail. If this is preventing you from moving ahead, just 
use -noappend and concatenate relevant output later.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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