Re: [AMBER] MD Analysis - Consistency

From: Daniel Roe <>
Date: Fri, 28 Dec 2018 09:33:39 -0500


On Sun, Dec 23, 2018 at 1:11 AM senal dinuka <> wrote:
> 1. Would consistency be a matter on publishing MD results?

This is a really broad question and difficult to answer, particularly
when we really only have a very vague notion of what you did and what
you're trying to accomplish. In general, consistency is key to
publishing results. All of your results should be reproducible.

> 2. Can we rely on rmsd fluctuation as a fact about stability, if not
> what other methods are better?
> 3. For analysis of hbond/gbsa how can we chose the frames, considering
> rmsd of ligands fluctuates drastically throughout the time in most case
> scenarios?

RMSD in most cases is a reasonable measure of stability, but it
depends on many factors such as what your reference structure is and
what the RMSD values actually are. For example, an RMSD to the first
frame that remains around 1.0 Ang and is flat for the simulation
indicates a relatively stable structure, whereas an RMSD to first
frame that increases to 4.0 Ang and seems flat may indicate an initial
change in conformation followed by stability, or it could be
fluctuating (since RMSD becomes less reliable the farther away you are
from your reference). Other measures of structural stability are RMSF,
native contacts, number of hydrogen bonds, cluster analysis, etc,
although none of these are necessarily "better" per se.


> Regards,
> Thank you
> --
> D L Senal Dinuka
> Grad.Chem., A.I.Chem.C.
> Research Assistant
> College of Chemical Sciences
> Institute of Chemistry Ceylon
> Rajagiriya
> Sri Lanka
> +94 77 627 4678
> _______________________________________________
> AMBER mailing list

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Received on Fri Dec 28 2018 - 07:00:02 PST
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