OK, thanks for reply.
On 2014-05-27 00:40, Jason Swails wrote:
> 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
--
Sangita Kachhap
SRF
C/O Dr. Balvinder Singh
BIC
IMTECH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 27 2014 - 09:30:03 PDT
