[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

JPierre wrote:
> 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...

>    JPierre

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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