[gmx-users] Numbering in xtc and in conf.gro. Does it coincide?

Vitaly Chaban vvchaban at gmail.com
Tue Jan 20 15:56:12 CET 2009

> Source code file: matio.c, line: 533
> Fatal error:
> Lo: 0.000000, Mid: 1.000000, Hi: 1.000000
> Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
> adequate.
> However what could the above error indicate?

>that all atoms belong to the same cluster.

Yes, it's true in my case.

And one more question about index file. If xtc-qrps is used and only
the groups of interest are output in xtc file, should the atoms in the
index file be renumbered or not?

For example, if in conf.gro we have atoms of interest with numbers 4,5,6
and didn't write atoms 1,2,3 to the xtc file, should we then refer to the
wanted atoms as 4,5,6 (as it was initially) or 1,2,3 (due to the

In other words, is information about the initial (in conf.gro)
numbering of molecules present in the xtc trajectory file? Looking at
the xtc using gmxdump I see the numbering always start with zero in
spite of the xtc-qrps arguments.

Thank you.

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