Re: [DIYbio] Entire Cell Simulator

On Mon, Mar 04, 2013 at 09:38:24PM -0800, Koeng wrote:

> Although I was kinda wondering about cell simulation on the molecular
> scale... Like a program that folds proteins inside a simulated cell and all

You don't know what you ask for. The fastest thing on Earth for
that should be currently http://en.wikipedia.org/wiki/Anton_(computer)
and it's limited to short times (17 us) and reasonably
small systems (23 kAtoms).

A nice package to play with is VMD/NAMD http://www.ks.uiuc.edu/Research/namd/
which also has GPGPU support (you're probably got to need that,
unless you've got a few kNode Beowulf in your basement).

> the chemicals react with each other and this stuff. I think this would take
> too much computing power though

You can say that again. And MD is a very high level of theory,
things turn awful fast as you reach down.

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