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

[João Henriques]

Just one more thing. If you're following Justin's tutorial, I guess you're
using lysozyme. This protein will not deviate very much from it's crystal
structure at 27ºC, let alone at -40ºC (*in the context of a molecular
dynamics simulation**). I understand that it may be possible to
experimentally unfold this protein reversibly using low temperature and
high pressure, but this may be unfeasible to perform using a regular
protein force field and water model. It will not behave as you expect.

* I should add that this is a very stable protein and the disulfide bonds
(which cannot be broken during the simulation) make it almost impossible to
unfold it completely at any temperature using molecular dynamics.

/J



On Wed, Jun 7, 2017 at 7:15 PM, João Henriques <joao.m.a.henriques at gmail.com
> wrote:

> ​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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>