Re: Different trajectories with and without restarting

From: Axel Kohlmeyer (
Date: Fri May 15 2015 - 18:26:53 CDT

On Fri, May 15, 2015 at 7:09 PM, Grzegorz Nawrocki <> 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.


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
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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