[gmx-users] Another shuffling question ..

Marc Baaden baaden at smplinux.de
Wed May 1 14:33:24 CEST 2002

Hi David,

thanks for your comment, but now I am a bit confused ..

spoel at xray.bmc.uu.se said:
>> I'm sorry to say that there is no desort option... But sort will only
>> work on "fermion" molecules: it will interchange two waters or two
>> ions but not a water and an ion. So once you have sorted, there is no
>> way back. 

So if I interpret this rightly, then you might have a problem when you
use -sort plus -shuffle and want to look at a deshuffled trajectory ?

To give a practical example:
I have the original system, which I use to create tpr files and eg index
files needed for analysis.

Now the original run is shuffled + sorted and so indices in the index
files and in the trajectory will not correspond.

With "deshuffling" I can reverse the shuffling, but not the sorting, so
now my indeces should correspond to the right moleculetype (eg protein
is protein, water is water, ions are ions), but if I want to address eg
a specific water molecule from my index file, it might have another
number due to sorting, so you would have to recreate the index files
from the deshuffled trajectory ?

Is this correct? Does it make sense ? Or am I talking rubbish ?

The overall message would then be: you have to create your index files
from the final trajectory that you want to analyze, once it was simulated
and deshuffled, and not from the starting point.


 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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