VMD-L Mailing List

From: Lubos Vrbka (shnek_at_chemi.muni.cz)
Date: Thu Sep 11 2003 - 16:34:59 CDT

dear scott,

> I am trying to make a movie of my simulation where in each frame the
> protein is superposed back on the first frame. No problem there except
> that in some frames a ligand that is bound to the protein is wrapped
> around the periodic boundary while the protein is not. So in the movie,
> it looks like every so often the ligand jumps off the protein. Is there
> any way to get that molecule back in its proper place?It is a constant
> pressure simulation, so the box size changes, which I would imagine
> makes it hard to wrap the ligand back around. Any suggestions?
i don't know what software do you use for your simlation runs, but the
solution that i always use with my amber trajectories is "imaging" the
trajectory with the ptraj software (part of the amber software package).
it does exactly what you need - puts all parts of the system inside the
box. i don't know what programs can be used for such operation on
non-amber trajectories, but i'm sure that google with "image trajectory"
and name of your software as keywords should help.

maybe it's possible to workaround this problem inside vmd, but i
wouldn't recommend it. it's always better to image the trajectory before
analysing/viewing it, because the problem you're describing here can
cause serious problems with some analysis programs (for example, these
programs can tell you that your ligand jumped 20A away and back in 1
fs... that is of course impossible).

hth,
lubos 

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Mgr. Lubos Vrbka
Center for Complex Molecular Systems and Biomolecules
J. Heyrovsky Institute of Physical Chemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
shnek_at_chemi.muni.cz
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