[gmx-users] grompp Input/Output Error

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 30 21:38:11 CEST 2010

Peter Nash wrote:
> Hey,
> I'm a new GROMACS user using 4.5.1... I'm working through whatever 
> tutorials I can find to learn the program.  I'm having major problems 
> using grompp... No matter which tutorial I'm working through, when I run 
> the program to create a .trp file, I get an input/out error message.
> I'm going to use the offical Water demo as an example.  I have the 
> conf.gro , spc216.pdb, topol.top, and grompp.mdp files in the default 
> directory.  I run grompp using the following command line from within 
> the directory with the necessary input files:
> /home/[usr]/bin/gromacs/bin/grompp -v -f grompp.mdp -c conf.gro -p 
> topol.top -o topol_full.tpr
> I've also tried running it without the -v tag... Just to experiment.  
> When I enter the above command, I get the following output in the terminal:
> Ignoring obsolete mdp entry ‘title’
> Ignoring obsolete mdp entry ‘cpp’
> Ignoring obsolete mdp entry ‘domain-decomposition’
> Replacing old mdp entry ‘unconstrained-start’ by ‘continuation’
> Ignoring obsolete mdp entry ‘dihre-tau’
> Ignoring obsolete mdp entry ‘nstdihreout’
> Ignoring obsolete mdp entry ‘nstcheckpoint’
> Sorry couldn’t backup mdpout.mdp to ./#mdout.mdp.1#
> Program grompp, VERSION 4.5.1
> Source code file: futil.c, line: 459
> File input/output error:
> mdout.mdp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I'm not sure why the program is having an issue here since I'm following 
> the manual exactly. I also get a similar error whenever I try to run 
> grompp using any other .mdp file as well... No idea what the program is 
> telling me, either.
> If anyone could give me input on this error, I'd greatly appreciate it.  
> Thank you!

Looks like you don't have write permissions in the directory where you're 
running grompp.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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