Hi, 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, Ramon
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