On 5/31/18 1:26 PM, Amin Rouy wrote:
Thanks Justin.
I find in some literature that RMSD is not a good parameter to specify
equilibrium from it. (e.g.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145956/).
So what is the best parameter I should rely on to find the dynamic
equilibrium?
Ultimately you have to show that whatever structural properties you are
interested in are not still changing over time.
-Justin
On Thu, May 31, 2018 at 7:23 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 5/31/18 1:18 PM, Amin Rouy wrote:
Hi everyone,
The results of simulation show all quantities are at equilibrium, like
energies, temperature, density, etc. But RMSD is increasing all the time
and not reaching an equilibrium.
Does it mean should I wait longer?
Thermodynamic properties converge quickly. Dynamic properties do not
necessarily. Temperature converges within a few ps, but a protein's
dynamics may take thousands or millions of times longer to converge. Don't
rely solely on RMSD to make this assessment; it is a degenerate metric.
-Justin
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