[gmx-users] rmsd,

[Justin Lemkul]

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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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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