RE: Restarting trajectories

From: Bennion, Brian (
Date: Wed May 20 2015 - 10:42:46 CDT

Hello All

I possibly missed reading earlier posts, but I just want to make sure that the restart files that seem to be causing issues are indeed binary restart files.
I imagine that they are, but just want to clarify.


From: [] on behalf of Michael Feig []
Sent: Wednesday, May 20, 2015 12:47 AM
Subject: namd-l: Restarting trajectories

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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