On Sun, May 25, 2014, Sangita Kachhap wrote:
>
> Is it possible to do MD simulation at constant pH and temperature range
> 50-55 degree Celsius simultaneously?
The thermostats in Amber allow you to specify a single (target) temperature,
not a range of temperatures. If you really need a range, I'm guessing you
would have to run a series of simulations at various temperatures of interest,
and average the results. But a single simulation at the center of you
temperature range would be a good place to start.
The implicit solvent GB models in Amber were parameterized for 25 C; I don't
know of any work testing these at higher temperature. If you are new to Amber
(or to constant pH simulations) I'd recommend getting some experience with
implicit solvent models first, before trying more difficult calculations.
....dac
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Received on Mon May 26 2014 - 07:30:02 PDT
