Re: [AMBER] sampling issue

From: Carlos Simmerling <>
Date: Mon, 19 Jul 2021 10:14:07 -0400

can you be more specific? "sampling" is a very general term. it usually
applies to the idea that biomolecules and other flexible molecules have
multiple local energy minima, and for mayn types of simulations you need to
"sample" those minima (move between them, possibly searching for the
lowest-energy minimum, or possibly getting the relative populations of the
minima, depending on the project goal). The sampling problem usually means
that it is difficult during an affordable simulation to cross the barriers
between minima and generate a properly Boltzmann-weighted ensemble.

For your comment about RISM, it may refer to sampling all of the possible
positions of the explicit water molecules. This can be less difficult than
sampling the biomolecule conformations, but still takes time for the water
and ions to move around and try all possible arrangements. A method like
RISM avoid this sampling problem for the solvent, but not the solute.

On Sun, Jul 18, 2021 at 2:29 PM angad sharma <>

> Hello everyone,
> I am not able to realize the literal meaning of the sampling issue in MD.
> There is a sampling issue in MD that's why we prefer RISM. I am not able to
> visualize the sampling issue.
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Received on Mon Jul 19 2021 - 07:30:03 PDT
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