[gmx-users] Generate an Index File

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 13 03:11:41 CET 2009

Jack Shultz wrote:
> I am trying to run g_dist
> c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr
> -------------------------------------------------------
> Program g_dist, VERSION 4.0.5
> Source code file: futil.c, line: 330
> File input/output error:
> index.ndx
> -------------------------------------------------------
> Thanx for Using GROMACS - Have a Nice Day
> so I tried mdrun with the -dn option
> mdrun.exe -dn -v -x -deffnm md
> It failed to generate an index file. What am I doing wrong?

You're using the wrong tool; make_ndx is used to make index groups (hence the 
name).  The -dn option of mdrun is some special function, apparently related to 



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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