[gmx-users] rmsd,

[Amin Rouy]

I am studding phase diagram a liquid crystal (my own molecule). So I see
the final structure has some ordering as I expect (as you say I should
expect as scientist), but RMSD does not reach any stable value.why?

So my question is can I rely on what I expect !? or I must proof the
equilibrium by showing specific dynamic property, if so what that can be?

On Thu, May 31, 2018 at 7:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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