[gmx-users] gmx convert-tpr problem

Gregory Man Kai Poon gpoon at gsu.edu
Thu Apr 6 00:43:20 CEST 2017

Hello all:

I am having problems extending my runs using convert-tpr in GROMACS 2016.1.  In the latest instance, for example, I have a 100-ns run that I want to extend to 200 ns.  I used the convert-tpr command to get my new .tpr file:

gmx convert-tpr -s md_0_100.tpr -until 2000000 -o md_100_200.tpr

With the new .tpr file in hand, I start mdrun:

gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_0_200

At this point I get this error:

GROMACS:      gmx mdrun, version 2016.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/i5/EXTREME 64/AGC_GTG2
Command line:
  gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_100_200

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_100.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:

Program:     gmx mdrun, version 2016.1
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)

Fatal error:
File appending requested, but 4 of the 4 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 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 checked, double-checked, triple-checked that all the files the error is referring to is in the working directory.  In fact, all the files (the md_0_100.* files from the previous run) as well as md_100_200.tpr are in the same folder (the working directory), in which the mdrun command is invoked.  Any suggestions would be appreciated.

Kind regards,


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