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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 15 22:59:55 CET 2007

Hi Bob,

This would give an intolerable decrease in performance, because of the
neighbour searching thing.

I had a routine which might be of help, but unfortunately somewhere in
the process of "improvement" I broke it and didn't return to it again.
Maybe I can have a look at it some moment these days (but don't expect
it to be a panacee).



On 3/15/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
> 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
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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