[gmx-users] rmsd,

[Justin Lemkul]

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
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

==================================================