[gmx-users] gmx convert-tpr problem

Justin Lemkul jalemkul at vt.edu
Thu Apr 6 01:23:02 CEST 2017

On 4/5/17 6:43 PM, Gregory Man Kai Poon wrote:
> 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:
>   md_0_100.log
>   md_0_100.xtc
>   md_0_100.trr
>   md_0_100.edr
> -------------------------------------------------------
> 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.

The error message could probably use a bit of re-wording, but what mdrun is 
telling you is that the .cpt file tells mdrun that there should be md_0_100.* 
that are being written, but your use of -deffnm md_100_200 means the output 
files will be named md_100_200.* and mdrun is trying to append to the existing 
files with different file names.  Use -noappend if you're changing the output 
file names.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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