VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Mon Feb 14 2005 - 10:29:45 CST

hi,

i have one more question, this time regarding the display (and analysis)
of structures with Periodic Boundary Conditions. if i load such a
structure (e.g. amber trajectory) to amber and specify
        within 10 of (resid X)
i get perfect results for "resid X" located in the center of the box.
however, when "resid X" is close to the box boundary, PBS conditions are
not taken into account, i.e. residues in larger distance than 1/2 of the
box are not (correctly) reported as fulfilling the condition.
i suspect that "measure contacts" command works in the same way like
"within" selection macro (however i haven't tested that). this would
result in incorrect (smaller) number of contacts reported for residues
near the box boundary.

i know that easy way of treating such problem might be imaging of the
trajectory, but even this procedure may fail on some special occasion.
however, i do it for proteins now. for salt solution, i would have to
image the trajectory for every single ion in the unit cell...
is there any way how to address this problem?

thank you for hints. with best regards
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Complex Molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
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