simulation methods

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simulation methods

Postby Janka27 » Thu Apr 26, 2012 10:32 pm

Hello,

I would like to know what kind of simulation methods are applied at F@H to study the folding/unfolding of proteins? MD, some kind of modified MD, or non full-atom methods?

Thanks,
Janka
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Re: simulation methods

Postby Jesse_V » Thu Apr 26, 2012 10:49 pm

Welcome to the forum Janka27!

There are some experts on this forum that know more about this than I do, but I know that they use statistical models. Since it isn't really described on the folding.stanford.edu page, I think that a good place to start is here: http://en.wikipedia.org/w/index.php?tit ... gnificance
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Re: simulation methods

Postby 7im » Thu Apr 26, 2012 11:09 pm

Looking at the FAQs would be a good start.

MDs such as Gromacs, ProtoMol, and Amber are shown/discussed. FAH uses mostly Gromacs currently, but has used many different menthods over the years.

Also search for Markov State modeling, Implicit Solvation, Explicit Solvation... on the FAH site, this forum, NEWS page... or their respective WIKI pages.
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Re: simulation methods

Postby Janka27 » Fri Apr 27, 2012 7:08 am

:) thanks a lot for the tips and info!
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