aminrou1986 at gmail.com
Thu May 31 19:27:03 CEST 2018
I find in some literature that RMSD is not a good parameter to specify
equilibrium from it. (e.g.
So what is the best parameter I should rely on to find the dynamic
On Thu, May 31, 2018 at 7:23 PM, Justin Lemkul <jalemkul at 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 A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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