[gmx-users] yet another question about PBC...

Ramon Crehuet rcsqtc at iiqab.csic.es
Mon Jun 30 17:16:54 CEST 2008

Please don't flame me for asking yet another question about the "out of
the box" and PBC issue. I've tried to RTFM, RTFML, but could not find
the question I'm asking.
I (think) I understand what PBC implies and the fact that "out of the
box" makes no sense because the system is periodic and gromacs treats
the periodicity correctly. However, when calculating the rmsd of a
trajectory with g_rms with respect to the protein I get a warning:
"cannot make broken molecules whole without a run input file, don't
worry mdrun doesn't write broken molecules".
and the rmsd has unrealistic jumps when the chains of the protein (a
tetramer) leave the box (but if I calculate distances with g_bond, they
are always ok)
If I correct the trajectory with trjconf -pbc nojump, the new trajectory
seems to behave as expected.
So my questions are, i)should I worry about the warning? ii) why does
g_rms not treat PBC as expected? Should I use some options?
Thanks in advance,

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