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
know.
I use multiple trjconv with PBC treatment to dirty fix that ...
Which may be fine for your particular application...
JPierre
--
David.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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