[gmx-users] SHUFFLING tutorial

[Bert de Groot]

David van der Spoel wrote:
> 
[...]

> If your standard dsehuf.ndx for a system of N atoms starts with:
> [ deshuf ]
> 0 1 4 6 7 etc.
> you have to modify it to the old format:
> 1 N
> deshuf N
> 0 1 4 6 7 etc.
> 
> You only have to change the top bit, not the actual numbers. An
> alternative is to modify it to be:
> [ deshuf ]
> 1 2 5 7 8 etc.
> 
> That wouldn't be too hard with a script either.
> 


alternatively, you can run the attached utility to (re)generate a deshuffling
index file. The only thing you need is two .gro files with the same 
coordinates in different order (use e.g. editconf to get the coordinates
from your .tpr file in a .gro file):

./deshuf ordered.gro shuffled.gro > deshuffle.ndx

good luck,

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________
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