[AMBER] Completely fixed atoms in MD Simulation (pmemd)

From: Melisa Averina <maverina.ucsd.edu>
Date: Mon, 18 Jan 2016 12:03:36 -0800 (PST)


I am trying to simulate a very large protein but I am only interested in
the dynamics of only a small region of the protein that binds to an
external molecule. I was wondering if we can save an enormous amount of
computational effort by holding the entire protein completely fixed to its
original structure except for the small portion I am interested in, i.e.,
integrate the equations of motion of only those atoms belonging to this
small portion, so most of the inter-atomic forces are not even evaluated
(saving a lot of time).

I have read about belly, freeze, and shake but I believe they use some
kinds of restraints, as so it won't help in accelerating the simulation

I would really appreciate your advise on this.

Thank you!!


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Received on Mon Jan 18 2016 - 12:30:04 PST
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