[gmx-users] deletion of some water molecules

Thomas Piggot t.piggot at soton.ac.uk
Tue Aug 31 14:51:57 CEST 2010

You can use trjorder to do this



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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