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From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Wed Jan 18 2006 - 08:08:41 CST
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hi guys,
i asked already once but didn't get any replies, so i'm trying it once more.
i need to create all 26 periodic images of a set of atoms, or better to
say, i need to create all 26 periodic images surrounding a simulation
box. is there a way how to do that?
what do i need it for? i need to count the number of hydrogen bonds
every molecule forms with its neighbors. the problem is that the
respective commands in the vmd (measure hbons, for example) are not PBC
enabled. so creating all periodic images of the central simulation box
is one of the ways how to treat it.
it should then work like:
for N in central_box
for M in central_box_and_all_replicas
measure hbonds of N with M
i would be really glad if someone could help me. i tried to have a look
in the manual, but nothing seems to be appropriate for this task. (doing
this analysis for every frame in the trajectory should be the easy part
of the task)
thanks,
lubos
-- ..................................................... 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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