[gmx-users] rescaling PBC for PDB output

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 15 10:35:01 CEST 2003

On Mon, 2003-04-14 at 16:54, 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.

Your new box wouldn't be periodc anymore, so this is not entirely
trivial (although it would be easy to code). Furthermore your protein
may diffuse. What you can do is to
order the trajectory (trjorder) to sort them according to distance to
the protein. Drawback is that you will have different water molecules at
each step.

> Many thanks in advance for any suggestion or help.
> Cheers,
> -----------------------
> 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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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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