VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Fri Dec 09 2005 - 10:41:37 CST

hi guys,

i would like to use vmd to analyze a trajectory of water freezing. the
desired 'output' is the following:
1) water molecules in the liquid phase would be colored normally (i.e.
oxygen red, hydrogen white)
2) water molecules incorporated into the ice lattice would be colored
differently (e.g., dark blue and light blue for oxygen and hydrogen,
respectively)

i'd like to distinguish between liquid and solid by means of hydrogen
bonds (or coordination number) - water with 4 neighbors tetrahedrally
oriented in proper distance (with some tolerance, of course) would be
regarded as ice.

if it will work, it would be nice to have one more feature. the color
would be changed to 'ice' when a water would have 4 tetrahedrally
oriented neighbors for some time, let's say 10 frames (and vice versa).

the question is - is there something already written i could use? if
not, what would be the best way to do it?

thank you in advance for help. 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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