Re: a question about equilibrium

From: Joshua Adelman (
Date: Wed May 21 2008 - 21:07:35 CDT

Hi Jin Tao,

Maybe a better criteria of equilibration for proteins that have
flexible regions that undergo conformational changes is to look at the
RMSD of a smaller domain of the protein. Also when you talk about
transitions between two states of the protein being "likely", you have
to keep in mind the appropriate time scales associated with that
process. Unless the protein is sampling a large population of states
on the nanosecond time scale, you're much more likely to see the
characteristic behavior of the RMSD settling to a stable value.

My best advice though is to partition your protein into what you would
consider to be stable domains and then look at the relative RMSD for
that domain alone. These issues tend to be system specific so without
an idea of what type of protein you are looking at, along with the
conditions (initial selection of coordinates, etc), it is hard to give
a definitive answer.

Best wishes,

On May 21, 2008, at 6:32 PM, <> <
> wrote:

> Hi, all
> I have a question about running equlibrium. In NAMD tutorial, it
> says
> "you would like to know if your protein is conformationally stable.
> For
> this, you will calculate the RMSD of the protein backbone. This will
> give
> you an idea of the stability of the protein. If the RMSD is still
> increasing at the end of the run, it means your protein is still
> searching for a lower energy state, and thus is not yet equilibrated!"
> According to my understand, I think it means that if the system is
> equilibrated the RMSD will be a horizontal line all the time, which
> seems
> to be a criterion in assessing the equilibration. But if the protein
> is
> likely to change between A state and B state, such as active site
> open and
> closed, the RMSD should be a horizontal line at first, then jump to a
> another horizontal line, isn't it? The conclusion seems to be
> contradictory to the criterion above. So I am puzzled and confused,
> there
> must be something wrong in my deduction, could somebody give a
> suggestion?
> Thanks at first!
> PS: I think the change bewteen A state and B state can happen in a
> thermodynamic equilibriation state. Is it wrong? the change must
> "transit"
> from a the equilibrious state to another?
> Jin Tao
> ���Ta���ſ�Ƭ�ɣ�
> *���ѹ�ƴ��д�ʼ����������
> ����������>>

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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