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

[Justin Lemkul]

On 6/7/17 12:50 PM, ZHANG Cheng wrote:
> 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?
> 

It is as Joao has said - that's just a coordinate file of a pre-equilibrated box 
of water that was generated using the SPC water model.  You can indeed use it to 
simulate other 3-point water model systems following an initial equilibration.

> 
> I am trying to see if my protein will be denatured in cold condition.
> 

The properties of the water model are going to be critical here.  For instance, 
SPC has a maximum density around -41 C, which is obviously very unphysical 
(water has a real maximum density at +4 C) so if you're seeking to model 
behavior at -40 C, then SPC is a very bad choice because its properties are not 
realistic.  I suggest you investigate the many possible water models that exist 
and find one or more that might reproduce some of the most important properties. 
  None of them gets everything right.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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