Angle criteria to add bound between two atoms

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1

Dear Axel,

Thanks for your response.
I want to use it for water molecules bounding according to the zhao’s paper entitled “Precursor Film in Dynamic Wetting, Electrowetting, and Electro-Elasto-Capillarity”, they mentioned that " We specified a hydrogen bond between water molecules if the O-O distance was less than 3.5 A ˚ and simultaneously the angle O-H…O was greater than 100 degree". So I need to check the O-H…O angle and O-O distance actively during the simulation in every several steps. For distance as I mentioned can use fix bond/create command but for angle I don’t have any idea. I think your mentioned ways are for fixed geometry not during the simulation.
do you mean these criteria have conflict with chemistry?

sincerely yours,
Abbas

please always reply to the mailing list and not only individual
people. thanks, axel.

2

Dear Axel,

Thanks for your response.
I want to use it for water molecules bounding according to the zhao's paper
entitled "Precursor Film in Dynamic Wetting, Electrowetting, and
Electro-Elasto-Capillarity", they mentioned that " We specified a hydrogen
bond between water molecules if the O-O distance was less than 3.5 A ˚ and
simultaneously the angle O-H.......O was greater than 100 degree". So I need
to check the O-H.......O angle and O-O distance actively during the
simulation in every several steps. For distance as I mentioned can use fix
bond/create command but for angle I don’t have any idea. I think your
mentioned ways are for fixed geometry not during the simulation.
do you mean these criteria have conflict with chemistry?

not the criteria, but how you want to apply them to modify your bond topology.
you seem to be confusing hydrogen bond *analysis* with actual force
field parameters and computing bonded interactions.
the fact, that the english used in the sentence you quoted has some
deficiencies encourages this kind of misunderstanding.

there is currently no hydrogen bond analysis feature in LAMMPS. but
there are external MD analysis and visualization packages, that have
this implemented.

axel.