[gmx-users] protein unfolding in water

[Justin Lemkul]

On 9/19/13 10:12 AM, fatemeh ramezani wrote:
> dear users
>
> I'm studying gold nano-particle effect on one of the blood protein stability and structure. one time I simulated the protein in the presence of  the gold nanoparticle and once without nanoparticles.
>
> when I simulated protein alone in water, I expected the protein to remain stable but protein RMSD, gyration,dssp and .... graphs show protein structure is changing and protein helices are opening during the simulation.
>
>   Thus, I can not study nanoparticle interaction effect on the protein structural changes , because the structural changes also observed  in the absence of nanoparticle.
> I think there is a problem. What is the solution you offer me? What is the problem?
>

If the model does not reflect reality, that suggests a deficiency in the force 
field, run settings, or system setup.  Since you've told us nothing about how 
you're doing the simulations, there's little advice anyone can offer.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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