On Mon, May 26, 2014 at 10:47 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>
> Thanks for reply.
>
> I have to do two different simulation at pH 5 & temperature 50 and pH 5
> & temperature 55 degree celcius. I don't have to do for range of
> temperature. So I was asking that is it possible to do MD at higher
> temperature at pH 5.
>
> Now I got the answer that constant pH is for 25 degree celcius.
>
To add on a little bit here, I have not seen too many published studies at
constant pH in which the temperature was set to a value significantly
different than 300 K. As Adrian mentioned, hydronium ion concentration
(autoionization of water) is temperature-dependent. For instance, the pKw
of water at 20 C is 14 (as expected), whereas at 50 C it is 13.26 (so
neutral pH is 6.63 at 50 C).
The first step that I would do if this was my study would be to titrate the
model compounds (ACE-AS4-NME, for instance) at 50 C and see how the
computed pKa compares to the experimental pKa of that compound _at that
temperature_. Of course you would need access to the experimentally
determined pKas of the capped amino acids at 50 C, but if you had that and
the results compared well it would be good evidence regarding the validity
of the model.
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 26 2014 - 12:30:02 PDT
