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 :-)
Mark
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