Restarting trajectories

From: Michael Feig (
Date: Wed May 20 2015 - 03:01:37 CDT

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

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.



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