[gmx-users] Urea parameterization

[David van der Spoel]

On Thu, 2005-03-03 at 16:56 +0200, Alexander wrote:
> Hi All!
> I have performed the molecular dynamic for 9ns of protein in 2M and 6M Urea solutions. The literature data estimate the values of secondary structure (b-sheet) as 80-90% and 0%-10% repetitively. But measured values from this dynamic are 85% and 80%. Is anybody having any ideas about this error? I have used GROMOS96FF with urea topology from gromacs suit. The starting structure was taken from crystal data.
> Thank you.
SImulate longer, raise the temperature.
> 
> Best regards,
>  
> Alexander Yakovenko
> Institute of Molecular Biology & Genetic of NAS of Ukraine
> 03143
> acad.Zabolotnogo str. 150
> Kiev
> Ukraine
> ______________________________________________
> E-mail: yakovenko_a at ukr.net
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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