[gmx-users] rmsd,

[Justin Lemkul]

On 5/31/18 1:32 PM, Amin Rouy wrote:
> could you please specify exactly which properties I should check?

No, because this is your job as a scientist and is the kind of thing you 
should plan long before ever doing a simulation. What are you interested 
in observing? What are you testing? That motivates what you need to analyze.

> because I do not have any clue of the final structure,

The "final" structure is entirely arbitrary and depends on when you 
happen to stop the simulation. It's the ensemble you care about.

> (besides if the structure does not change, not necessarily means it is
> stable, maybe is it stuck in unstable phase)

A structure won't get stuck in an "unstable" state, as that is, by 
thermodynamic definition, not likely to occur. Your bigger problem is 
getting stuck in an energy well. This is a central challenge in MD 
simulations and there is a ton of literature about it. Again, that's 
your homework to do before you even start doing a simulation of your own.

-Justin

>
> 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
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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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

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