[gmx-users] gmx convert-tpr problem

[Gregory Man Kai Poon]

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

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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 > 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 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 search the archive at > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Cgpoon%40gsu.edu%7Ccd5f1661e0be4bfea85608d47c7b0a58%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636270315275689367&sdata=DpOZWBaO5Sr6Jt5JLKNXIU6Vj4AIrM%2Ba61T4OKeyvO8%3D&reserved=0 before > posting! > > * Can't post? 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