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

[ZHANG Cheng]

Dear Joao,
Thank you very much for your support. I am following Justin's tutorial but simulating a fragment of antibody (Fab).


I will try the different water models.


Yours sincerely
Cheng




------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Thu, Jun 8, 2017 01:07 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>; 

Subject:  Re: Re:  Simulate protein at subzero condition in aqueous buffer



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"<gromacs.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