[gmx-users] rescaling PBC for PDB output

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Tue Apr 15 17:23:01 CEST 2003

That sounds great!

My parents worked so much that I was born tired :).  I have to re-read the
Manual (it's all there).

Thank you very much!

On Tue, 15 Apr 2003, Anton Feenstra wrote:

> Alan Wilter Sousa da Silva wrote:
> > Hi List!
> >
> > 	I have a simulation with a lot of water. I just wonder if I could
> > use trjconv to generate a PDB output with box smaller than the original
> > one (just covering protein for example) and with water within the box, but
> > excluding the waters outside the new box.
> I don't think trjconv can 'cut' away molecules outside the box.
> It wouldn't be too difficult to implement, you might try that yourself.
> But, another option is to use trjorder. trjorder can sort molecules
> with respect to their distance to a reference group. So, you can get
> your water sorted in order of distance to the protein, so the first
> water molecules in the output trajectory will be in a layer around
> the protein. Then you should estimate how many water molecules you
> want to keep, that will correspond to the thickness of the water
> layer you will keep. You should make an index file with one group
> containing your protein (and ligands) and the first so many waters
> that you want, and possibly counter ions. trjconv can then make yet
> another new trajectory where only a layer of water remains.

Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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