[gmx-users] gmx convert-tpr problem

[Mark Abraham]

Hi,

Yep.

If you want to end up with a series of numbered parts, then mdrun -noappend
is useful.

Mark

On Thu, 6 Apr 2017 02:43 Gregory Man Kai Poon <gpoon at gsu.edu> wrote:

> Hi Mark,
>
> To clarify, I should be calling mdrun like:
>
> gmx mdrun -s new.tpr -cpi old.cpt -deffnm old
>
> ?
>
> I apologize ahead if this sounds obvious.
>
> Kind regards,
> Gregory
>
> G
>
> et Outlook for Android<https://aka.ms/ghei36>
>
>
> From: Mark Abraham
> Sent: Wednesday, April 5, 19:25
> Subject: Re: [gmx-users] gmx convert-tpr problem
> To: Discussion list for GROMACS users
>
> Hi, As the messages suggest, if you would like to change the output names,
> you can't append. If you would like to append, don't change the output
> names. The old output files are there, but you've told mdrun to expect them
> to have different names, and to append to them, but used a checkpoint file
> that has different names. It doesn't know whether the error was in you
> using the wrong checkpoint file, or a mismatching output name, or that
> there are missing files, or that you don't want appending. Mark On Thu, 6
> Apr 2017 00:43 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 > appendi
>  ng 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
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%7Cgpoon%40gsu.edu%7Ccd5f1661e0be4bfea85608d47c7b0a58%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636270315275689367&sdata=wud%2BY7HyhMxHQhwPzSzJ836fq8vKy%2FUj9BjZ0EMscBY%3D&reserved=0
> > -------------------------------------------------------
>  > > > 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, > > Gregory > > -- > Gromacs Users mailing list > > * Please
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