Using MMB with large RNA molecules

Easily model the structure and dynamics of macromolecules
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Juan Antonio Raygoza Garay
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Joined: Wed Aug 10, 2011 12:51 pm

Using MMB with large RNA molecules

Post by Juan Antonio Raygoza Garay » Fri Nov 04, 2011 2:29 pm

Questions related to modeling large >1k nucleotide
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Juan Antonio Raygoza Garay
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Joined: Wed Aug 10, 2011 12:51 pm

Re: Using MMB with large RNA molecules

Post by Juan Antonio Raygoza Garay » Fri Nov 04, 2011 2:30 pm

How can i use "Physics where is needed" in order to cope with very large ran molecules in MMB?
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Samuel Flores
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Joined: Mon Apr 30, 2007 1:06 pm

Re: Using MMB with large RNA molecules

Post by Samuel Flores » Fri Mar 08, 2013 9:11 am

I don't recommend turning on "Physics where you want it" for entire molecules, certainly not for large ones. The issue is that MMB is not very fast at doing MD.

Turn this feature on only for a very small region of your model -- a few residues maybe.
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