Justin Lemkul jalemkul at vt.edu
Sun Dec 31 05:48:26 CET 2017

On 12/30/17 11:44 PM, Neha Gupta wrote:
> At first, I gave,
> gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc
>   I selected "system" for output
> It says
> Program gmx trjconv, VERSION 5.1.4
> Source code file:
> /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c,
> line: 1322
> Fatal error:
> Index[6376] 6377 is larger than the number of atoms in the
> trajectory file (6376). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Which index number should I select for all the three commands mentioned
> above?

No command is going to work if the contents of the .tpr and .xtc do not 
match. Either you've mixed up your files or you didn't save all 
coordinates during the run, in which case you need to make a matching 
.tpr file. gmx check may provide some clues, but at present it's hard to 
know what has gone wrong.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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