Re: [AMBER] Clustering VS constant rmsd

From: David A Case <>
Date: Wed, 17 Oct 2012 21:09:53 -0400

On Wed, Oct 17, 2012, vaibhav dixit wrote:

> Checking rmsd is an essential part of the MD trajectory analysis and it
> helps us to validate if the system has reached equilibrium (converged) i.e.
> expected to be closer to what would a real protein/DNA/any other system
> would be.

I think you need to be careful here. "Convergence" of a simulation
means that it has relaxed into a structural basin that represents what the
force field thinks the protein ought to be doing. This might be a long way
from what the "real" protein does. If the starting structure is derived from
good experimental data, conformations seen after equilibration may well be
further away from the "real" result than the starting structure. And the
longer you run, the worse things may get.

[Of course, none of these reservations apply to those using Amber(tm) force


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Received on Wed Oct 17 2012 - 18:30:02 PDT
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