From: Grzegorz Nawrocki (aksonik_at_gmail.com)
Date: Mon May 18 2015 - 15:04:17 CDT
Dear Bradley, Axel and Jeff,
Yes, the same seed is in my configuration files for the restarts as for the
but I suppose that in the former the seed is neglected,
since I provide initial velocities and comment the line with the initial
I am pretty sure of it, because using different seeds in restart
I get exactly the same trajectories.
I assume that turning on tCouple I use Berendsen thermostat, not Langevin.
Am I right?
Does using floating point generate only tiny differences? I noticed that
simulations are not repeatable working with much bigger system
- it consists of about 30,000 atoms. Using Berendsen thermostat
the entire system accelerates in one direction. I suppose that this is
as the "flying ice cube" problem. This is clearly visible when the
simulation is continous,
but not when it is divided into shorter runs with restarting.
Trajectory of the entire system seems to be altered in the restart points.
Is a way to avoid "flying ice cube" problem, but not by simply removing net
I have tried to increase the temperature bath coupling parameter, but
2015-05-16 1:06 GMT-04:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> On May 16, 2015 4:08 AM, "Grzegorz Nawrocki" <aksonik_at_gmail.com> wrote:
> > 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?
> Like I already told you, they do come from using floating point math and
> the langevin thermostat.
> > 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>
> >> >
> >> > 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
> >> > system - it consists of two atoms. I used a single core, temperature
> >> > coupling, constant volume and mostly default parameters. Please find
> >> > 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
> >> > 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
-- Grzegorz Nawrocki
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