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Re: [lammps-users] Considering pH effect in LAMMPS
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Re: [lammps-users] Considering pH effect in LAMMPS


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 27 Jun 2017 16:02:38 -0400

On Tue, Jun 27, 2017 at 3:50 PM, Amin Koochaki
<aminkoochaki1987@...24...> wrote:
> Dear Axel,
>
> Thanks for your quick reply.
>
> I have tertiary amine and ester group in the backbone of my polymer. I know
> that the amine groups can be protonated.

then you should do the same thing that people do when simulating
proteins with such functional groups:

you do not really change the pH of the solvent, but rather the
protonation state of the solute. for that you need to lookup/determine
the pKa or pKb constants for the respective functional groups and then
the protonation state is determined by the pH of the solvent. there
should be tutorials and plenty of discussions in forums for MD
simulation of proteins. the classic example is the protonation state
of histidine groups.

axel.

>
> Amin
>
>
> On Tue, Jun 27, 2017 at 5:10 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>>
>>
>> On Tue, Jun 27, 2017 at 8:33 AM, Amin Koochaki
>> <aminkoochaki1987@...24...> wrote:
>>>
>>> I want to reduce the pH of polymer/water system and investigate the
>>> effect of this reduction on some properties.
>>>
>>> How can I reduce the pH of solution by LAMMPS?
>>
>>
>> does your polymer have functional groups that could be protonated or
>> deprotonated?
>>
>> axel.
>>
>>
>>>
>>>
>>>
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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.