[gmx-users] Deshuffling atoms vs. residues

[Jerome Henin]

Okay, now I have a partial answer to my own question. Apparently, when using 
the -sort and -shuffle options, the indexfile written by grompp undoes the 
shuffling, but not the sorting, so to speak. This became clear when I noticed 
that using just -shuffle without -sort produced the very same indexfile.

So let me replace my original question with two and a half questions:
1) Is this the intended behavior, and if so, what's the idea behind it?

2) How can I restore the original order?

Thanks,
Jerome

On Monday 31 July 2006 14:42, Jerome Henin wrote:
> Hi,
>
> I suspect this might be a stupid question, but we've all been beginners one
> day, haven't we?
>
> I have generated a shuffled/sorted trajectory (grompp -sort -shuffle) of a
> lipid bilayer, which I have then deshuffled using trajconv and the index
> file. In the resulting file, each residue is in one piece again, but the
> order of residues seems to be still different from the original one.
> Do you have an idea why this happens?
>
> Thanks a lot,
> Jerome