[gmx-users] Bug ? PBC in g_dist
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jul 21 09:25:03 CEST 2006
> Hi all,
> I am studying the fusion of small aggregates that can occur near the
> crossover point of my PBC. So for measuring distances between two of
> these objects I have defined 2 groups, each containing several
> monomers. Each time a monomer crosses the wall of the box, g_dist does
> not consider the periodicity to calculate the correct COM of the
> corresponding aggregate. I got artificial distance fluctuation in the
> measured distance.
> Is there a solution to correct this behavior ?
this is an ill-defined problem, that I tried to fix in the trjconv -pbc
cluster algorithm with partial success only. It depends for instance on
the definition of your aggregates. Furthermore you may have "periodic"
aggregates (e.g. a lipid membrane spanning the box).
If you have suggestions how to solve it *in general* then please let us
> I use multiple trjconv with PBC treatment to dirty fix that ...
Which may be fine for your particular application...
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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