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

From: Jason Swails <>
Date: Mon, 18 Jan 2016 16:12:16 -0500

On Mon, Jan 18, 2016 at 3:03 PM, Melisa Averina <> wrote:

> Hello,
> 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
> itself.

​You need to define what you mean by "accelerate the simulation". If you
constrain a large fraction of the degrees of freedom (which is what belly
does -- it uses constraints, not restraints), then you substantially reduce
the size of phase space. This reduces the amount of sampling needed to
characterize the relevant parts of phase space, meaning you can more fully
characterize your model with fewer time steps.

Indeed, this results in a substantially cheaper model. It also changes
that model a lot and makes it a lot less realistic. So the added
simplicity may (and probably will) come at the cost of accuracy.

However, you seem to be equating "accelerating the simulation" with taking
less time per time step. This is impossible in Amber. There's a bigger
problem, though, with the underlying assumption that will significantly
reduce the feasibility of this approach -- the commonly-used potential
energy functions in molecular dynamics are not pairwise decomposable, and
so you cannot simply omit certain pairs of interactions to save time in the
general case.

For GB or PB, the GB radii or dielectric boundary affects all pair-pair
interactions, but are determined by all atoms in the system. So you can't
eliminate redundant interactions as much as you think you can. For PME,
the reciprocal space calculation itself is entirely non-local, as it is
performed in Fourier space. Sure, you can simplify some of the
direct-space calculation and eliminate some interactions, but you'll still
be limited by the PME part.

The savings in your proposed scheme would come not from the reduced cost of
each time step, but rather the vast reduction in the number of degrees of
freedom. But they would come with a cost.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 18 2016 - 13:30:03 PST
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