[gmx-users] convergence of MD simulations,

[Ali Alizadeh]

Dear Justin,
Thank you very much for your reply and especially your time.
According to my structural analysis my convergence sounds good as you
mentioned, my diffusion coefficients, RDF, number density profiles over
different time intervals show stable states.

Ali Alizadeh

Justin wrote:

Neither temperature nor total energy tells you anything about
convergence.  They
are related instead to the stability of the various algorithms employed during
the simulation.  In fact, one can manipulate these quantities rather easily by
tweaking settings inappropriately.

Convergence is more rigorously assessed through physical observables in your
system.  For a simple fluid, do its properties (density, diffusion constant,
RDF) change over different intervals of simulation time?  If they do, the
simulation isn't converged.  For biomolecules, looking at any number of
structural properties can be informative.  By your criteria above, my
multi-domain heterodimeric protein complex was converged after about 5 ns.  In
reality, it underwent large, cyclical transitions over the course of 500 ns.


-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> |
(410) 706-7441http://mackerell.umaryland.edu/~jalemkul




On Tue, Aug 19, 2014 at 7:00 PM, Ali Alizadeh <ali.alizadehmojarad at gmail.com
> wrote:

> Dear All users,
> I have been engaged in answering this question"how long should we continue
> calculating to make sure we can get justifiable results?". Are there any
> suggestions to dig out to find out when a system converges? I know this is
> a too general question.
> In case of my systems(confined structure, interface between fluid and
> solid) after 1ns simulation my temperature fluctuation shows quite
> convergence, my total energy corroborates this convergence too.
>
>
> --
> Sincerely
>
> Ali Alizadeh
>



-- 
Sincerely

Ali Alizadeh