AMBER Archive (2009)

Subject: Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration

From: Cihan Aydin (cihan.aydin_at_umassmed.edu)
Date: Sat Jun 27 2009 - 09:29:21 CDT

I encountered this e-mail while roaming on the reflector. I'll cite a
paper that helped me much.

Stella,L.; Melchionna,S.
J. of Chem. Phys., Vol. 109, No.23, 1998

Cheers,

Cihan

On Thu, 2009-05-28 at 14:15 -0400, Carlos Simmerling wrote:
> that's way too general. it depends on many things, such as the quality of
> the experimental structure, the difference in conditions between your
> simulation and the experiment (pH, solvent, ions etc) and where in the
> structure the rmsd values come from. rmsd is a very broad measure and a
> value of 2 may mean that all regions differ by about 2, or that many differ
> by 1 and others differ by a larger number (for example 5, or maybe 10). rmsd
> itself is only 1 measure of simulation quality so I strongly disagree that
> simulation rmsd values should "not be greater than 2". if you do get larger
> values, though, you should find out why and see if there is a way to
> validate that the behavior is reasonable.
>
> equilibration can be very tricky and there is no one "correct" protocol we
> can give. it depends again on the initial structure and any differences in
> your simulation conditions from the expt. it is entirely possible to have
> most of the structure look ok, but due to bad placement of an H atom or even
> an ion, part of the initial structure will be incorrectly modeled and the
> simulation will not give a good model. equilibration can help with these but
> you need detailed information about differences between MD and experiment to
> proceed. we tend to be cautious and use about 10 steps in our general
> equilibration procedure, and more when anything was modeled (such as a side
> chain or a ligand).
>
>
> On Thu, May 28, 2009 at 2:08 PM, nicholus bhattacharjee <
> nicholusbhattacharjee_at_gmail.com> wrote:
>
> > Thank you Bill. But you did not answer my second question. Is the rmsd
> > value
> > between the initial structure and the final structure be not more than 2
> > Armstrong.
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> >
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-- 
Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student @ Schiffer Lab

364 Plantation St. LRB 970M
Worcester, MA 01605

cihan.aydin_at_umassmed.edu
+1 (508) 856-3430

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