[gmx-users] rmsd,

[Amin Rouy]

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?

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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>