[gmx-users] request

[Dallas Warren]

The error states what the problem is, there are three files that the
program expects to be in the directory, but they aren't.

Two things can do, change the command line if it is doing not what you
want it to (i.e. it is trying to add more data onto an existing
simulation, or you have used the wrong file names) or return the files
to the directory so that it can append data to them.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 5 December 2017 at 06:32, Rakesh Pant
<rakesh.pant at students.iiserpune.ac.in> wrote:
> 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:
> md_0_1.log
> md_0_1.xtc
> md_0_1.edr
>
> -------------------------------------------------------
> 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
> 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.
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