please always reply to the mailing list and not only individual
people. thanks, axel.
On Tue, May 8, 2018 at 1:39 AM, abbas abouei <abbasabouei@...16...
> 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,
> A.Abouei Mehriz
> On Monday, May 7, 2018, 10:33:00 PM GMT+8, Axel Kohlmeyer
> On Mon, May 7, 2018 at 6:03 AM, abbas abouei via lammps-users
>> Dear lammps users,
>> I would like to apply the bound between two water molecules with two
>> criteria at the same time, one the distance between two oxygen atoms and
>> secone the angle of O-H.....O in Lammps. The distance criteria can be
>> by fix bond/create command but I dont have any idea about how I can add
>> angle criteria. do you have any recommendation?
> tinkering with the bonding topology is best done outside of LAMMPS.
> complex operations will require some programming, so that would be
> easier to do with some suitable scripting language. reading/parsing of
> LAMMPS topology data can be done with different tools. for example,
> there is Pizza.py, which is python based, and there is VMD, which uses
> Tcl scripting.
> what you want to do is very uncommon (and in conflict with chemistry,
> too). also, i am wondering whether you have considered the implication
> of adding this bond in terms of exclusion of non-bonded interactions.
> how many of these special bonds do you need to create and what is
> their overall purpose? if my crystal ball is correct, adding them to
> the topology may not be producing the effect you are looking for.
>> A.Abouei Mehriz
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> Dr. Axel Kohlmeyer akohlmey@...24... http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
Dr. Axel Kohlmeyer akohlmey@...24... http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.