[gmx-users] PBC and large hydrogen-bonded molecules

mernst at tricity.wsu.edu mernst at tricity.wsu.edu
Tue May 23 00:31:58 CEST 2006

Hello fellow Gromacs-users,

Today I was extracting PDB snapshots from a solvated DNA 12mer simulation trajectory.
When I went to view the snapshots, I saw that one of the DNA strands suddenly jumped
some nanometers away from its partner during certain frames. I remembered that there was
a note about fixing this artifact in the trjconv documentation, and soon found that the
-whole or -nojump options produced an easier-to-view snapshot series.

However, viewing a few original snapshots with water left in place, I was struck more
forcefully by how an entire strand jumps when even part of it reaches the boundaries of
the current simulation box. A colleague who saw the original snapshots was concerned,
and seemed to think that both DNA strands should jump together if they were going to
jump at all. I didn't think it was a problem apart from needing an extra command line
switch when converting trajectories.

You can see it happen here in the original snapshot extraction, with both strands in the
same box with solvent:

and then one strand jumping:

Is there anything wrong with just one strand of the DNA jumping? I didn't think so,
since Gromacs makes whole molecules jump but the 2 strands of DNA are not held together
by explicit bonds. It looks strange to have one strand almost entirely outside the
central box, while no water molecules lurk out there, but I have formerly presumed that
this has no special physical significance and looks strange only because the DNA strand
is a much larger molecule.

I would appreciate opinions on whether or not the jumping of a single strand can be
regarded as a mere visual/implementation artifact or whether it represents a compromise
of simulation correctness.

Matt Ernst
Washington State University

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