[gmx-users] SHUFFLING tutorial

[Dallas Warren]

David,

Thank you very much for that.  I finally got it all to work :-)

Here is what I did:
         # added 1 to all the index numbers in the deshuf.ndx that was 
generated by grompp, wrote a quick script to do that
         # used the deshuf+1.ndx to deshuffle the trajectory files with trjconv
         # generated a new_topol.tpr using grompp with the initial 
simulation files (md.mdp, conf.gro, topol.top etc.) and without -sort and 
-shuffle
         # generated a deshuffled_index.ndx using make_ndx with new_topol.tpr
         # then used the files as required by the various analysis tools

Was all error free and worked like a charm :-)

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083