[gmx-users] rmsd,

[Amin Rouy]

could you please specify exactly which properties I should check?
because I do not have any clue of the final structure,
(besides if the structure does not change, not necessarily means it is
stable, maybe is it stuck in unstable phase)

thanks Justin

On Thu, May 31, 2018 at 7:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <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
>>>
>>> --
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>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
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> ==================================================
>
> 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
> http://www.thelemkullab.com
>
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