[gmx-users] Urea parameterization

[Alexander]

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.

Best regards,
 
Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
03143
acad.Zabolotnogo str. 150
Kiev
Ukraine
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E-mail: yakovenko_a at ukr.net