Dear Prof. Case,
Yes, I agree with you that there is no "real" structure.
The longer the MD, the further is it away from the starting geometry. Thus, it is really hard to find a converged state.
I guess it is the reasons why more people using clustering to do the analysis. However, if it is the case, do we still really need to exclude those so-called "equilibrium state" conformers. If afterall, we are trying to get as much conformers as possible for clustering analysis.
What is your opinion on this?
Best regards,
Catherine
> Date: Wed, 17 Oct 2012 21:09:53 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] Clustering VS constant rmsd
>
> 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
> fields....]
>
> ....dac
>
>
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Received on Wed Oct 17 2012 - 20:00:02 PDT
