Bernhard Knapp wrote:
1) trjconv with the "-pbc nojump" option does not help - it removes most
If I understand correctly, -pbc nojump will help when the relevant atoms
are part of the same [moleculetype]. One fragment in each of your two
examples is apparently the same four-strand sheet with helix wrapped
around it. This suggests to me that you might have several chains, each
as a different [moleculetype] and your observations are actually what
you should expect. If so, -pbc cluster is the kind of thing you should
be using.
In any case, a description of the composition of your system and copies
of a series of commands that reproduces your result would always have
been appropriate :-)
Mark
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