[gmx-users] desorting

[Chris Neale]

I have seen a script to generate a .ndx file for desorting.
http://www.gromacs.org/pipermail/gmx-users/2002-May/001546.html

Many later posts continue to suggest that there is no gromacs tool to 
desort. e.g.
http://www.gromacs.org/pipermail/gmx-users/2006-August/023109.html

I realize that the mentioned script is not an official gromacs tool, I 
just want to be sure that there are no other problems. Am I correct that 
if one could generate the correct .ndx file (i.e. assuming the top 
script is correct) the trajectory can be properly deshuffled and desorted?

My basic strategy is this:

make_ndx -o original.ndx (for analysis tools)
loop{
  grompp -shuffle -sort -o shuffledsorted.tpr
  trjconv -s shuffledsorted.tpr -o shuffledsorted.gro
  script original.gro shuffledsorted.gro > deshuffledesort.ndx
  mdrun
  trjconv -f shuffledsorted.xtc -n deshuffledesort.ndx -o original.xtc
  trjcat -f complete_original.xtc original.xtc -o complete_original.xtc
}