On 4/21/2011 8:00 AM, Peter C. Lai wrote:
I have a fairly stupid question about restart from a checkpoint and binary
identical messages, probably because I can't understand the doco.
When I restart (or extend) a double-precision run from a checkpoint involving
either dlb or even a different decomposition count (say I changed the number of
parallel threads), I get a message that says it restarted but the
trajectory is not binary identical.
My question is: I assume this trajectory will continue from the last set of
double-precision coordinates and velocities in the cpt file? What is the
loss in precision/error propagation of the resulting trajectory as compared
to if I started the entire run from the begining? (say I am extending my
trajectory from 1ns to 10ns). I guess I understand that both trajectories
would be "equally valid" but not binary identical, but what does this mean
in terms of things like ultimate RMSD measurements and so forth? I don't
necessarily care that the two concatenated trajectory files will not cmp to
zero.
These issues are discussed here
http://www.gromacs.org/Documentation/Terminology/Reproducibility
There's no *loss* upon continuation with a new DD, it's just that it is
almost guaranteed to be different from what would have resulted from
continuing with the old DD. In the limit of an infinite situation, both
would converge to the same ensembles.
Makr
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