VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Fri Dec 09 2005 - 01:51:37 CST

hi,

> if the hbonds of interest lie on the inter-image of the PBC boxes, it
> already indicates that the simulation is at risk -- proteins move across
> the boundary of the box, ....
don't know whether i got your question right... from the methodological
point of view, there is nothing wrong with the fact that the solute is
present near/at the simulation box boundary or crossing it. the boundary
position depends on the origin of the coordinate system and this is
arbitrary. the md-code will handle this using the pbc.
of course this can create problems with programs that do not have 'pbc
aware' analysis tools (e.g., vmd). the current thread is here to solve
these problems.

> if the objects of interests are all contained in the main image, then
> the suggested additions are not useful.
partially, yes. this is however not true in all cases (periodic solids,
for example).

all the additions would perfectly solve the situation when the part of
the system of interest is close/at the boundary. then, it wouldn't be
necessary to, e.g., image the trajectories and center the solute of
interest in the simulation box. you'd just tell vmd 'use PBC for
distances, ...' and it would work.

another example: i have 2 peptides in the a solution. i want to analyze
ion distribution around both peptides. in the standard way, i have to
image & center the trajectory with respect to the first peptide, then do
the analysis; then image & center with respect to the second peptide and
do the analysis again. this is really not very effective, but i can do
it. but what if i want to calculate distribution of ions around 50
individual objects in the unit cell?

i think for me the 'pbc awareness' (defined with respect to this thread)
is the most missing feature in the vmd code (that is almost perfect
anyway:-)).

regards,
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
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