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Re: [lammps-users] Angle criteria to add bound between two atoms
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Re: [lammps-users] Angle criteria to add bound between two atoms


From: abbas abouei <abbasabouei@...16...>
Date: Tue, 8 May 2018 06:11:25 +0000 (UTC)

 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





On Tuesday, May 8, 2018, 1:40:31 PM GMT+8, Axel Kohlmeyer <akohlmey@...24...> wrote:


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...> wrote:
> 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
> A.Abouei Mehriz
>
>
>
> On Monday, May 7, 2018, 10:33:00 PM GMT+8, Axel Kohlmeyer
> <akohlmey@...24...> wrote:
>
>
> On Mon, May 7, 2018 at 6:03 AM, abbas abouei via lammps-users
> <lammps-users@...404...rceforge.net> wrote:
>> 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
>> added
>> by fix bond/create command but I dont have any idea about how I can add
>> the
>> 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.
>
> axel.
>
>
>
>
>> Bests,
>> Abbas
>>
>> 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.