[Computational-biology] (no subject)

michael walshe mick.walshe at gmail.com
Wed Dec 14 12:23:50 EST 2005

Dear Sir

My name is Michael Walshe & I am a final year chemical engineering student
in Dublin, Ireland. As part of my final year research project I will perform
molecular dynamics simulations on the protein streptavidin to see the
effects pressure & temperature will have on the protein in water. For this
we used the Gromacs package to perform the analysis. We found bizzare
results regarding the radius of gyration - it decreased with time as the
simulation progressed, even at 400 & 500 K. Most runs were performed for 1
ns. We used the program g_gyrate from Gromacs to analyze this. Although the
radius of gyration decreases, the root mean square deviation of the C-alpha
atoms increases. All literature data contradict the fact that the radius of
gyration would increase at such high temperatures. I cannot come to any
conclusions about this behaviour due to my limited knowledge on the
area.Would you be able to offer some explaination for this happening?

Thank you for your time

Michael Walshe

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