From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 29 2021 - 10:01:01 CDT
On Fri, Oct 29, 2021 at 10:43 AM Monika Kumari <
> Dear all,
> I am running a well-tempered metadynamics simulation with 2 fs timestep
> using NAMD which is running fine but when I restart the run, it gives the
> rattle algorithm error. What can the possible things I might be
> overlooking. Please suggest.
If the instability is only at the restart, can you confirm that you are
also loading the correct .colvars.state file alongside the correct NAMD
(If you used a NAMD patched with Plumed, you can follow the corresponding
instructions for restarting).
> Though after reducing the time step, the error disappears.
> Also, when I ran two simulations parallelly with exactly same files, the
> colvar trajectory was different. Being molecular dynamics a deterministic
> simulation, how could it happen?
This is false. Even with a completely deterministic set of options, the
limited precision of floating-point math adds tiny errors that are
completely harmless for the sake of physical accuracy but lead over time to
diverging trajectories. And if you use a non-deterministic thermostat or
barostat (very common in NAMD) determinism may go out the window from the
very first step.
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