[gmx-users] request

Rakesh Pant rakesh.pant at students.iiserpune.ac.in
Mon Dec 4 20:32:11 CET 2017

What is -s md ? in the command line.

On 05-Dec-2017 12:32 AM, <mmahmoudig at razi.tums.ac.ir> wrote:

hi.what causes this error?

Command line:
gmx mdrun -s md -cpi md_0_1_prev.cpt

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_1_prev.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 2016.3
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
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
original run. Checkpointing is merely intended for plain continuation of
For safety reasons you must specify all file names (e.g. with -deffnm),
all these files must match the names used in the run prior to
since we will append to them by default. If the files are not available,
can add the -noappend flag to mdrun and write separate new parts. For
concatenation of files, you should use the gmx trjcat tool instead.
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