[gmx-users] question about continuation using tpbconv and mdrun -cpi
Mark.Abraham at anu.edu.au
Thu Jul 30 18:18:46 CEST 2009
Baofu Qiao wrote:
> Hi Berk,
> Thanks for pointing out my mistake!
> What I worry about is how big the deviation is after several continuations? If
> it is unpredictable, it is a sad news.
The objective is to avoid perturbing the system *with the restart*. Any
perturbation will make the trajectory sufficiently far in the future
unrecognizable from the unperturbed one, i.e. chaotic. However such a
perturbation that is small enough that it does not disturb the ensemble
will lead to results that are statistically identical to the unperturbed
system. For example, you could add up the forces on the atoms in the
opposite order, which perturbs the system through rounding error, but
(ought) not shift the ensemble. Dynamic load-balancing achieves a
Non-reproducibility in the integrator can be acceptable if the above
condition is true. Hence all my previous advice - by all means check
that you can achieve reproducibility over restarts, but ignore it for
production simulation, unless you actually need it.
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