[gmx-users] Another shuffling question ..

[Marc Baaden]

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.

  Marc


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 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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