From: Grzegorz Nawrocki (aksonik_at_gmail.com)
Date: Fri May 15 2015 - 21:08:40 CDT
Dear Bradley and Axel,
First of all, thank you very much for your quick responce. For me it is
just the beginning of using NAMD. I am grateful for your help. Second, I
heard about "butterfly effect" and I know that the distribution of the
various states is the usable output. However, I expected that no
differences should exist, even tiny, for exact restart. I am also aware of
introducing "randomness" into the system by using temperature control and
setting seed, but I do it only at the beginning, and the beginning is the
same for the simulations with and without restarting. Providing coordinates
and velocities I should be able to get exactly the same trajectory from any
checkpoin. Where do these tiny differences come from?
Best regards,
Grzegorz
2015-05-15 19:26 GMT-04:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> On Fri, May 15, 2015 at 7:09 PM, Grzegorz Nawrocki <aksonik_at_gmail.com>
> wrote:
> >
> > Dear NAMD users,
> > I have noticed that NAMD does not generate the same trajectory when a
> > simulation is run with and without restarting. I tested it using very
> simple
> > system - it consists of two atoms. I used a single core, temperature
> > coupling, constant volume and mostly default parameters. Please find the
> > enclosed input files for a short simulation.
> >
> > Without restarting NAMD everytime generates the same trajectory, as well
> as
> > with restarting, but both trajectories, i.e. with and without restarting,
> > are becoming more and more different with every restart.
> >
> > Is it a bug or I set something wrong?
>
> MD is chaotic and thus trajectories *have* to exponentially diverge
> over time when there is the tiniest difference (ever heard the term
> "butterfly effect"?). restarting enforces such tiny differences. the
> usable output of MD simulations are not the exact positions anyway,
> but the *distribution* of the various states that are visited over
> time. you can look up details in text books on statistical mechanics
> and thermodynamics.
>
> axel.
>
> p.s.: you *can* have an MD code that produces exactly reproducible and
> reversible trajectories, but then you'll have to do: 1. fixed point
> math, 2. only time integration and not thermostat, 3. fixed volume.
>
>
>
> >
> > Best regards,
> > --
> > Grzegorz Nawrocki
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
-- Grzegorz Nawrocki
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:08 CST