Re: Restarting trajectories

From: Axel Kohlmeyer (
Date: Wed May 20 2015 - 10:49:11 CDT

On Wed, May 20, 2015 at 9:47 AM, Michael Feig <> wrote:
> To come back to the different trajectory topic raised by Grzegorz and maybe
> clarify things:
> We do understand issues about the chaotic nature of MD simulations but it
> seems that a ‘short’ simulation, let’s say for 10 ps running on a single
> core should be identical

please note that the parallelization and load balancing methodology
used in NAMD will likely change the order in which forces are summed
even when running on a single processor. like it stated before, unless
you use fixed point math and no thermostat, you cannot expect
trajectories to be perfectly reproducible and reversible.

> whether it is run as a single run or restarted in between. If that is not
> the case with NAMD, it means that the frequency of restarts affects the
> trajectory one obtains.
> Moreover, we seem to see that every restart leads to some kind of reset in
> system drift which means that the results are actually different depending
> on how often
> simulations are restarted. We seem to see this with the Berendsen thermostat
> where (Langevin) random seeds should not play a role.
> The next step for us would be to dig into the NAMD code to see what is going
> on, but I think there may be a problem here.

have you checked the NAMD documentation whether there is an option to
remove the COM motion upon (re)start?
i wouldn't be surprised if this may be active by default and would
need to be disabled if you want to preserve the center of mass motion.
but in any case, i don't think removing the COM drift on restart
should be a big issue, but rather what part of your simulation setup
is *causing* it, since that should not happen under normal
please also note that unlike langevin, a berendsen thermostat will not
dissipate a drift but is more likely to enhance it
(since *all* velocities are scaled by the same factor thus having the
largest error on the fastest atoms).


> Michael.

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

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