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

Visvaldas K. coyote_v2002 at yahoo.com
Tue Dec 22 16:54:17 CET 2009

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?)

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


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