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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: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 8 May 2018 15:47:01 -0400

On Tue, May 8, 2018 at 2:11 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?

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.

>
>  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@lists.sourceforge.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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>>> lammps-users@lists.sourceforge.net
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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.



-- 
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.