[gmx-users] index.ndx files

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 31 01:44:02 CEST 2012

Eduardo Oliveira wrote:
> Hi,
> I'm trying to set up a configuration file to but i keep gettin an error 
> after the grompp_d run. I'm using the command line as follows:
> grompp_d -f stpr.mdp -c sistema_boxwater.gro -p sistema.top -o 
> sistema_stpr.tpr -n
> Text in bold correspond to my files.
> This is what i got:
> File input/output error:
> index.ndx
> Any ideas how to solve this?

The use of -n, in the absence of an explicit file name, causes grompp (or any 
other Gromacs program, for that matter) to search for the default file name, 
which is "index.ndx" in this case.  The error indicates that no such file exists 
in the working directory.



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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