[gmx-users] Reordering of a large GRO file - how

[Jernej Zidar]

Hi.
  I used editconf to replicate a small lipid bilayer patch, after
editing the topology file I'm able to simulate it. I have one small
question/issue.

  I would like to use g_membed to add a large molecule into the water
section (SOL) but editconf operates in such a way that it just
replicates the initial system, thus my SOL section is not continuous
but is scattered all over the GRO file hence the command fails.

  Is there a smart way to "reorder" so the SOL section would be
continuous*? How does GROMPP parse the GRO file?

  The topology file now looks like this:
A 34345
B 25
SOL 10000
A 34345
B 25
SOL 10000
...

Thanks in advance,
Jernej Zidar