[gmx-users] Including urea in simulations?

[Tsjerk Wassenaar]

Eugenia,

I fail to understand how this ties in with your subject, stating
something about urea. Please have the subject of your mail reflect the
question you ask.

As for guanidinium chloride. Guanidinium you can take from the
arginine side chain and chloride is natively part of the force field
anyway. Unfolding depends on many parameters, including size of the
protein and the time scale.

Cheers,

Tsjerk

On 2/6/07, Eugenia Polverini <eugenia.polverini at fis.unipr.it> wrote:
> Dear all,
>
> anyone knows if it is possible in Gromacs to perform protein unfolding
> simulations with the Guanidinium chloride in a box of water ?
> Thanks in advance!
>
> Eugenia
>
>
> --
> Eugenia Polverini, Ph.D.
> Dept. of Physics
> University of Parma
> Parco Area delle Scienze, 7/A
> 43100 Parma
> ITALY
>
> Phone: +39 0521 905254
> Fax: +39 0521 905223
> E-Mail: eugenia.polverini at fis.unipr.it
> http://www.fis.unipr.it/~polveri
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623