[gmx-users] Simulate protein at subzero condition in aqueous buffer

[João Henriques]

Hello,

"spc216.gro" is not a water model, it's just a pre-equilibrated simulation
box (300 K and 1 bar) with the coordinates of 216 3-site water molecules.
SPC and TIP3P are two examples of 3-site water models. Water model
properties are well studied and tabled (e.g.
http://aip.scitation.org/doi/10.1063/1.1862245).

I am no expert in pure water simulations, but I doubt 3-site water models
can reproduce ice in a realistic way. Will the force field even hold at
that temperature? I really don't understand why you'd want to try something
like this. However, and to finish, there's one thing I can tell you for
sure: your system will be much more "stable" at -40ºC. Why, because it will
barely move from it's initial conformation, due to the very low thermal
energy. In sum, you'll spend computational time sampling almost nothing.

Best regards,
João

On Wed, Jun 7, 2017 at 4:01 PM, ZHANG Cheng <272699575 at qq.com> wrote:

> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous
> buffer, to see if it becomes more stable than the elevated temperature
> (e.g. 65 C). Can I ask what is the valid temperature range for water
> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
> system as liquid state instead of frozen state? Thank you.
>
>
> Yours sincerely
> Cheng
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