Re: Reg: Solvation box

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Sun Jun 02 2019 - 08:28:21 CDT

Adupa,
  Perhaps this would help. Think about what pH 7.4 means. approximately 1
in 10^7 water molecules are split into a H+ and OH- units. How many water
molecules are in your simulation? 10K, 100K, 1M? If so, you would not see
a difference between plain water and the pH 7.4 solution.
Depending upon the molarity of your buffer, you might also add some
phosphate ions to your simulation. But again, think about the size of your
computational region to determine if that generates a reasonable
concentration of buffer.

As recommended by Pratik, the protonation state of the protein is the
feature that reflects the change in your environmental conditions.

On Sun, Jun 2, 2019 at 8:08 AM Adupa Vasista <adupavasista_at_gmail.com> wrote:

> But will that effect my interactions with protein.
>
> I need to do simulation on Amyloid beta aggregate under physiological
> conditions. in experiments they recreated the physiological conditions
> using Phosphate buffer such that it maintains pH of 7.4
>
> Can I safely use water?
>
>
>
> On Sun, Jun 2, 2019 at 5:12 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>>
>>
>> On Sun, Jun 2, 2019 at 4:55 AM Adupa Vasista <adupavasista_at_gmail.com>
>> wrote:
>>
>>> I need to have phosphate buffer with pH 7.4 as solvent in my simulation
>>> .Is it possible?
>>>
>>
>> just use plain water.
>>
>>>
>>> Thank you
>>>
>>> --
>>>
>>> *A.VasistaM.Tech,Department Of Chemical Engineering,*
>>> *IIT Guwahati.*
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>
> --
>
> *A.VasistaM.Tech,Department Of Chemical Engineering,*
> *IIT Guwahati.*
>

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