[gmx-users] restarting from cpt and binary identical

[Peter C. Lai]

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.

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Peter C. Lai                 | University of Alabama-Birmingham
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