[gmx-users] rescaling PBC for PDB output

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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