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:
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
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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