[gmx-users] Writing Coordinates of Atoms Outside Primary Periodic Box

[Robert Johnson]

Hello everyone,
As I was discussing in a previous thread, I'm having problems
visualizing/analyzing an REMD trajectory of ssDNA. As I understand,
most tools for unwrapping PBC (i.e. removing the jumps from one side
of the box to the other) do so by detecting large displacements
between successive frames. These large displacements are then
considered jumps which are corrected for accordingly.

These tools do not work for REMD because this type of trajectory is
riddled with large displacements - both from atoms jumping across the
box but also due to the swaps between adjacent replica. Using these
tools on REMD trajectories leads to detection of erroneous jumps.

The easiest thing to do (in principle anyway) would be to modify
Gromacs so that it would write coordinates outside the primary
periodic box (i.e. not apply periodic wrapping to the coordinates).
Has anyone done this? If not, can anyone give me some pointers on
where to start?
Thanks,
Bob Johnson