[gmx-users] Deshuffling atoms vs. residues

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 1 16:08:20 CEST 2006

Jerome Henin wrote:
> 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?
Yes, performance.

> 2) How can I restore the original order?
Somehow sort your original file and get a desort.ndx from that, but 
there is no gromacs tool for that I'm afraid.

> Thanks,
> Jerome
> On Monday 31 July 2006 14:42, Jerome Henin wrote:
>>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,
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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