[gmx-users] trjconv mismatch

Mark Abraham mark.j.abraham at gmail.com
Wed Jan 14 09:09:48 CET 2015

On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo <quyviolet at gmail.com> wrote:

> Dear All,
> I have got this error while running trjconv from .xtc to .pdb file. The
> System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is
> the total number of Atoms in the System. The index.ndx was created from
> md.gro file, and I Chose #1 for Protein. I don't know where is the original
> error of the mismatch here
> Fatal error:
> Index[4622] 135978 is larger than the number of atoms in the
> trajectory file (36976). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> I would appreciate for any help.

Providing your actual command lines and interactive choices would help. If
you'd done the right things, you'd probably not be having a problem, so
we'll need to know what things you actually did. ;-)

Also, use gmx check on the .xtc and .tpr files, and less on the .ndx files
to see whether these files contain the things you think they do.


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