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

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 30 17:26:52 CEST 2008

Ramon Crehuet wrote:
> 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?

As far as the warning, it's due to the fact that you specified something 
like a .pdb or .gro file for the -s flag, and not the .tpr file.  Not so 
important in this case, but it would affect, for example, making 
molecules whole with trjconv.

As for the second part, perhaps someone else has better insight, but 
usually the quick answer is to compensate for PBC using trjconv, as you 
have.  I know there are a few messages about this in the list archives, 
but I think they usually end with "use trjconv."


> Thanks in advance,
> Ramon
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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