[BiO BB] molecular dynamics of nucleosome

[Dan Bolser]

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Cheers,
Dan.

On 9 November 2011 17:37, nikhil gadewal <ngadewal at yahoo.com> wrote:
> Dear all,
>
> I would like to do moelcular dyanmics of nuclosome complex consists of  histones ocatamer and 146 bp of DNA. The total amino acids are 773 +146 bp of DNA.
> I want to study the effect of histone variants on the size and shape of octamer which leads to change in DNA binding to octamer. The variation in the histone will be not more that 8-10 residues.
> Thus I would like to know how much simualtion time in nano-seconds will it require to converge the MD and able to see capture the change in octamer packaging leads to change in overall shape of histone. How this change can be monitored? Also how the DNA histone interactions can be measured?. Does nano or micro seconds simulation can be performed for such a big system on workstation with 2 GPU (Tesla from nvidia)? Or it will require big clusters?
> Please comments on my queries
> - Nikhil
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