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.
Sincerely,
Vis Kairys
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