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 <jalem...@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 <jalem...@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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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
jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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