You can use trjorder to do this

Cheers

Tom

leila karami wrote:
Dear gromacs users

I did simulation of protein-dna complex in a box with size 7,7,7. There are 5000 water molecule in this box. After full md simulation, I need a pdb or gro file containing only water molecules being exactly environment of pr-dna complex and not water molecules being in edges or rest of box.

Is there any way to do that?


--
Dr Thomas Piggot
University of Southampton, UK.
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