[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Dec 23 01:29:26 CET 2009

Visvaldas K. wrote:
> Dear GROMACS users and gurus,
> I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy.  I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces "clustered" compactly for some postprocessing,  using trjconv for conversion of trr/xtc into PDB format:
> "-pbc mol" option of trjconv: metal ions are far from the rest of the protein.
> -pbc nojump or -pbc whole: inhibitor far from the protein, metals are fine.
> -pbc atom or -pbc res: couple of residues are disattached from the protein; metals and inhibitor are fine.
> -pbc cluster: doesn't work (irrelevant?)

-pbc cluster should work with a suitable index group of 
protein+metal+inhibitor - that's what it is for.

Once that's done, you may want to re-run trjconv to apply other effects. 
Two-pass processing is often necessary.

> Also -center and -boxcenter don't seem to help...
> Can anybody suggest some tricks? I used octahedral box for my runs.

"don't seem to help" also doesn't help. We can't guess what it was about 
your inputs and outputs that was contrary to your hopes :-)


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