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

[João Henriques]

​Higher complexity water models such as TIP5P and so on are able to better
reproduce bulk water properties (please check the paper I linked in my
earlier email). However, these models require more computational effort
(due to the increased number of interactions) and may not work well in
conjunction with a protein (many protein force fields were developed to be
used with specific water models)​. As Justin said, none of them gets
everything right.

/J

On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699575 at qq.com> wrote:

> Dear Justin,
> Thank you very much. I will try the possible water models.
>
>
> Do you know if there are water models to resemble frozen state?
>
>
> Yours sincerely
> Cheng
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Thu, Jun 8, 2017 00:50 AM
> To:  "ZHANG Cheng"<272699575 at qq.com>; "gromacs.org_gmx-users"<gromac
> s.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  Re: Simulate protein at subzero condition in aqueous buffer
>
>
>
> Dear Joao,
> Thank you for your help and the paper link.
>
>
> I was following Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/lysozyme/03_solvate.html
> On that page, it says "spc216.gro as the solvent configuration for SPC,
> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water)
> after the solvation step. So I assume "spc216.gro" refer to all the
> three-point water models?
>
>
> I am trying to see if my protein will be denatured in cold condition.
>
>
> Yours sincerely
> Cheng
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Wed, Jun 7, 2017 10:01 PM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> Cc:  "ZHANG Cheng"<272699575 at qq.com>;
> Subject:  Simulate protein at subzero condition in aqueous buffer
>
>
>
> 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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