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

--
==================================================

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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